Starting phenix.real_space_refine on Fri Jul 19 02:59:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jva_36672/07_2024/8jva_36672.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jva_36672/07_2024/8jva_36672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jva_36672/07_2024/8jva_36672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jva_36672/07_2024/8jva_36672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jva_36672/07_2024/8jva_36672.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jva_36672/07_2024/8jva_36672.cif" } resolution = 2.81 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= -0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3862 2.51 5 N 1002 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6071 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1652 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "B" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1455 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 1 Chain: "F" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1972 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 15, 'TRANS': 227} Chain breaks: 6 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.27, per 1000 atoms: 1.03 Number of scatterers: 6071 At special positions: 0 Unit cell: (76.68, 73.44, 147.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1187 8.00 N 1002 7.00 C 3862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " 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 F 401 " - " ASN F 122 " " NAG F 402 " - " ASN F 165 " " NAG F 403 " - " ASN F 282 " " NAG F 404 " - " ASN F 234 " " NAG F 405 " - " ASN F 61 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 5.9% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.929A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.676A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 103 removed outlier: 4.016A pdb=" N GLN D 103 " --> pdb=" O PRO D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.904A pdb=" N SER B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.689A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.635A pdb=" N LYS F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.548A pdb=" N ASN D 97 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.613A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.665A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 118 removed outlier: 3.935A pdb=" N ASN A 137 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.066A pdb=" N TYR A 192 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 52 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.177A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.821A pdb=" N VAL B 152 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 27 through 30 removed outlier: 4.097A pdb=" N ALA F 27 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 227 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 47 through 55 removed outlier: 3.561A pdb=" N VAL F 47 " --> pdb=" O TYR F 279 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.994A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.547A pdb=" N SER F 172 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 141 through 145 removed outlier: 5.924A pdb=" N LEU F 141 " --> pdb=" O LEU F 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 215 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1923 1.34 - 1.46: 1599 1.46 - 1.58: 2671 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 6219 Sorted by residual: bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG F 405 " pdb=" O5 NAG F 405 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C5 NAG F 405 " pdb=" O5 NAG F 405 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C5 NAG F 403 " pdb=" O5 NAG F 403 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 6214 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.08: 206 107.08 - 113.80: 3392 113.80 - 120.53: 2229 120.53 - 127.25: 2558 127.25 - 133.97: 67 Bond angle restraints: 8452 Sorted by residual: angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 112.96 108.70 4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" C TYR B 103 " pdb=" CA TYR B 103 " pdb=" CB TYR B 103 " ideal model delta sigma weight residual 117.23 111.53 5.70 1.36e+00 5.41e-01 1.76e+01 angle pdb=" C PHE F 32 " pdb=" CA PHE F 32 " pdb=" CB PHE F 32 " ideal model delta sigma weight residual 115.89 110.98 4.91 1.32e+00 5.74e-01 1.38e+01 angle pdb=" N GLY B 149 " pdb=" CA GLY B 149 " pdb=" C GLY B 149 " ideal model delta sigma weight residual 110.87 115.91 -5.04 1.54e+00 4.22e-01 1.07e+01 angle pdb=" CA GLY A 66 " pdb=" C GLY A 66 " pdb=" O GLY A 66 " ideal model delta sigma weight residual 122.45 120.16 2.29 7.20e-01 1.93e+00 1.01e+01 ... (remaining 8447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 3391 16.77 - 33.54: 290 33.54 - 50.32: 53 50.32 - 67.09: 8 67.09 - 83.86: 4 Dihedral angle restraints: 3746 sinusoidal: 1516 harmonic: 2230 Sorted by residual: dihedral pdb=" CB CYS A 134 " pdb=" SG CYS A 134 " pdb=" SG CYS A 194 " pdb=" CB CYS A 194 " ideal model delta sinusoidal sigma weight residual 93.00 169.35 -76.35 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 134.15 -41.15 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA ASP A 167 " pdb=" C ASP A 167 " pdb=" N SER A 168 " pdb=" CA SER A 168 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 3743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 627 0.036 - 0.071: 207 0.071 - 0.107: 78 0.107 - 0.142: 32 0.142 - 0.178: 2 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG F 403 " pdb=" ND2 ASN F 282 " pdb=" C2 NAG F 403 " pdb=" O5 NAG F 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA GLU B 158 " pdb=" N GLU B 158 " pdb=" C GLU B 158 " pdb=" CB GLU B 158 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" C1 NAG F 402 " pdb=" ND2 ASN F 165 " pdb=" C2 NAG F 402 " pdb=" O5 NAG F 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 943 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 53 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 54 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 54 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 54 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 126 " -0.034 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 127 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 127 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 127 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 58 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 59 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.024 5.00e-02 4.00e+02 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 700 2.75 - 3.29: 5199 3.29 - 3.83: 8847 3.83 - 4.36: 10352 4.36 - 4.90: 19171 Nonbonded interactions: 44269 Sorted by model distance: nonbonded pdb=" OG SER F 94 " pdb=" OE1 GLU F 96 " model vdw 2.217 2.440 nonbonded pdb=" OG SER D 35 " pdb=" O ALA D 49 " model vdw 2.251 2.440 nonbonded pdb=" OD2 ASP F 40 " pdb=" NH2 ARG F 44 " model vdw 2.304 2.520 nonbonded pdb=" O ARG B 52 " pdb=" NH1 ARG B 71 " model vdw 2.310 2.520 nonbonded pdb=" O SER A 114 " pdb=" OG SER A 114 " model vdw 2.321 2.440 ... (remaining 44264 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 individual isotropic 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: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.780 Find NCS groups from input model: 0.080 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6219 Z= 0.246 Angle : 0.630 8.436 8452 Z= 0.349 Chirality : 0.044 0.178 946 Planarity : 0.005 0.063 1080 Dihedral : 12.608 83.859 2298 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.30), residues: 747 helix: 0.33 (1.21), residues: 16 sheet: 0.87 (0.32), residues: 283 loop : -1.18 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.001 PHE F 220 TYR 0.016 0.001 TYR A 140 ARG 0.003 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 ASP cc_start: 0.6254 (m-30) cc_final: 0.5410 (m-30) REVERT: F 158 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7841 (tmt170) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.3979 time to fit residues: 211.3744 Evaluate side-chains 78 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6219 Z= 0.276 Angle : 0.637 8.154 8452 Z= 0.330 Chirality : 0.045 0.184 946 Planarity : 0.005 0.055 1080 Dihedral : 5.889 49.056 934 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.95 % Allowed : 12.28 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 747 helix: 0.63 (1.31), residues: 16 sheet: 1.08 (0.32), residues: 280 loop : -1.24 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.004 0.001 HIS A 189 PHE 0.016 0.002 PHE A 118 TYR 0.015 0.001 TYR A 140 ARG 0.006 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7177 (tp40) cc_final: 0.6961 (tp-100) REVERT: F 158 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.7873 (tmt170) REVERT: F 169 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8010 (tp30) outliers start: 13 outliers final: 5 residues processed: 95 average time/residue: 1.2787 time to fit residues: 127.2283 Evaluate side-chains 80 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6219 Z= 0.196 Angle : 0.611 8.170 8452 Z= 0.309 Chirality : 0.045 0.210 946 Planarity : 0.005 0.051 1080 Dihedral : 5.303 39.498 934 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.80 % Allowed : 13.77 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.30), residues: 747 helix: 1.05 (1.38), residues: 16 sheet: 1.18 (0.32), residues: 280 loop : -1.15 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.001 PHE B 130 TYR 0.012 0.001 TYR B 94 ARG 0.007 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.7017 (tp40) cc_final: 0.6804 (tp-100) REVERT: F 158 ARG cc_start: 0.8400 (mtt-85) cc_final: 0.7851 (tmt170) REVERT: F 169 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: F 298 GLU cc_start: 0.7711 (tp30) cc_final: 0.7387 (tp30) outliers start: 12 outliers final: 7 residues processed: 83 average time/residue: 1.2392 time to fit residues: 108.0575 Evaluate side-chains 79 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 0.0770 chunk 32 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6219 Z= 0.259 Angle : 0.617 9.641 8452 Z= 0.313 Chirality : 0.044 0.183 946 Planarity : 0.005 0.050 1080 Dihedral : 5.003 36.064 934 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.99 % Allowed : 14.97 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.30), residues: 747 helix: 1.11 (1.38), residues: 16 sheet: 1.08 (0.32), residues: 282 loop : -1.08 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS B 35 PHE 0.016 0.002 PHE B 130 TYR 0.014 0.001 TYR B 94 ARG 0.006 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 158 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.7864 (tmt170) REVERT: F 169 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: F 298 GLU cc_start: 0.7728 (tp30) cc_final: 0.7318 (tp30) outliers start: 20 outliers final: 6 residues processed: 83 average time/residue: 1.3399 time to fit residues: 116.1830 Evaluate side-chains 76 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 0.0030 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 6219 Z= 0.455 Angle : 0.710 8.145 8452 Z= 0.367 Chirality : 0.047 0.196 946 Planarity : 0.005 0.053 1080 Dihedral : 5.527 39.129 934 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.99 % Allowed : 17.07 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 747 helix: 0.83 (1.42), residues: 16 sheet: 0.82 (0.32), residues: 285 loop : -1.19 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 148 HIS 0.006 0.001 HIS B 35 PHE 0.019 0.002 PHE F 220 TYR 0.017 0.002 TYR B 94 ARG 0.010 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: B 154 ASP cc_start: 0.7119 (m-30) cc_final: 0.6499 (m-30) REVERT: F 24 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8207 (mp) REVERT: F 158 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.7925 (tmt170) REVERT: F 169 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7913 (tm-30) outliers start: 20 outliers final: 9 residues processed: 79 average time/residue: 1.3655 time to fit residues: 112.8078 Evaluate side-chains 71 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6219 Z= 0.219 Angle : 0.644 10.619 8452 Z= 0.327 Chirality : 0.044 0.178 946 Planarity : 0.005 0.051 1080 Dihedral : 5.003 35.900 934 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.54 % Allowed : 18.56 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.31), residues: 747 helix: 1.11 (1.43), residues: 16 sheet: 0.98 (0.31), residues: 296 loop : -1.15 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE B 156 TYR 0.014 0.001 TYR B 94 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: F 24 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8166 (mp) REVERT: F 158 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.7894 (tmt170) outliers start: 17 outliers final: 6 residues processed: 78 average time/residue: 1.2969 time to fit residues: 105.8874 Evaluate side-chains 67 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain F residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6219 Z= 0.371 Angle : 0.696 9.697 8452 Z= 0.358 Chirality : 0.046 0.195 946 Planarity : 0.005 0.052 1080 Dihedral : 5.181 36.893 934 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.95 % Allowed : 19.76 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.31), residues: 747 helix: 1.18 (1.45), residues: 15 sheet: 0.76 (0.31), residues: 302 loop : -1.16 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.005 0.001 HIS B 35 PHE 0.016 0.002 PHE F 220 TYR 0.016 0.001 TYR A 140 ARG 0.011 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: F 158 ARG cc_start: 0.8494 (mtt-85) cc_final: 0.7913 (tmt170) REVERT: F 169 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7597 (tp30) outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 1.3196 time to fit residues: 95.7873 Evaluate side-chains 69 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6219 Z= 0.212 Angle : 0.643 9.367 8452 Z= 0.329 Chirality : 0.044 0.180 946 Planarity : 0.005 0.051 1080 Dihedral : 4.884 34.560 934 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.95 % Allowed : 20.21 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.31), residues: 747 helix: 1.33 (1.43), residues: 15 sheet: 0.93 (0.31), residues: 296 loop : -1.16 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.001 PHE F 220 TYR 0.014 0.001 TYR B 94 ARG 0.009 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: F 23 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5365 (tp-100) REVERT: F 158 ARG cc_start: 0.8448 (mtt-85) cc_final: 0.7914 (tmt170) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 1.2976 time to fit residues: 99.2938 Evaluate side-chains 70 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 130 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 197 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6219 Z= 0.215 Angle : 0.642 9.090 8452 Z= 0.327 Chirality : 0.044 0.192 946 Planarity : 0.005 0.060 1080 Dihedral : 4.724 33.185 934 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.65 % Allowed : 20.66 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 747 helix: 1.56 (1.46), residues: 15 sheet: 1.01 (0.31), residues: 294 loop : -1.16 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.003 0.001 HIS B 35 PHE 0.010 0.001 PHE F 220 TYR 0.014 0.001 TYR B 94 ARG 0.015 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: F 158 ARG cc_start: 0.8429 (mtt-85) cc_final: 0.7922 (tmt170) REVERT: F 169 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7535 (tp30) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 1.3393 time to fit residues: 99.5703 Evaluate side-chains 67 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6219 Z= 0.232 Angle : 0.648 9.112 8452 Z= 0.330 Chirality : 0.044 0.176 946 Planarity : 0.005 0.062 1080 Dihedral : 4.681 32.468 934 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.65 % Allowed : 20.36 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 747 helix: 1.63 (1.49), residues: 15 sheet: 0.96 (0.31), residues: 296 loop : -1.12 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.004 0.001 HIS B 35 PHE 0.011 0.001 PHE F 220 TYR 0.014 0.001 TYR B 94 ARG 0.015 0.001 ARG D 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.5214 (m-80) cc_final: 0.4813 (m-80) REVERT: F 158 ARG cc_start: 0.8439 (mtt-85) cc_final: 0.7922 (tmt170) REVERT: F 169 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7534 (tp30) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 1.3821 time to fit residues: 101.0749 Evaluate side-chains 67 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 169 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.087156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057163 restraints weight = 16671.484| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.94 r_work: 0.2899 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6219 Z= 0.316 Angle : 0.688 10.304 8452 Z= 0.352 Chirality : 0.045 0.186 946 Planarity : 0.006 0.097 1080 Dihedral : 4.922 33.986 934 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.80 % Allowed : 20.81 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.31), residues: 747 helix: 1.52 (1.47), residues: 15 sheet: 0.86 (0.31), residues: 296 loop : -1.18 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.005 0.001 HIS B 35 PHE 0.014 0.002 PHE B 156 TYR 0.015 0.001 TYR B 94 ARG 0.020 0.001 ARG D 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.86 seconds wall clock time: 54 minutes 23.68 seconds (3263.68 seconds total)