Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 18:24:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/08_2023/7wcr_32428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/08_2023/7wcr_32428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/08_2023/7wcr_32428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/08_2023/7wcr_32428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/08_2023/7wcr_32428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/08_2023/7wcr_32428.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 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 21 5.16 5 C 3094 2.51 5 N 800 2.21 5 O 965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "a GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 4880 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1563 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "a" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1690 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.14, per 1000 atoms: 0.64 Number of scatterers: 4880 At special positions: 0 Unit cell: (68.859, 87.44, 138.811, 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 21 16.00 O 965 8.00 N 800 7.00 C 3094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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=2.00 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " 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 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 672.6 milliseconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 7.3% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.042A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.530A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.963A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.966A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.648A pdb=" N SER a 91 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 89 removed outlier: 3.826A pdb=" N LEU b 89 " --> pdb=" O ALA b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 132 Processing helix chain 'b' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.921A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'a' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLU a 10 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR a 33 " --> pdb=" O ASP a 99 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET a 34 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLU a 10 " --> pdb=" O THR a 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.735A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.735A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.763A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL a 210 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR a 208 " --> pdb=" O HIS a 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.770A pdb=" N THR b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP b 76 " --> pdb=" O SER b 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 10 through 12 removed outlier: 7.079A pdb=" N LEU b 11 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU b 39 " --> pdb=" O TYR b 55 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR b 55 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP b 41 " --> pdb=" O LEU b 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 30 through 31 removed outlier: 3.732A pdb=" N LYS b 36 " --> pdb=" O TYR b 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 121 through 123 removed outlier: 3.562A pdb=" N SER b 121 " --> pdb=" O PHE b 140 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL b 138 " --> pdb=" O PHE b 123 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU b 184 " --> pdb=" O VAL b 137 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS b 139 " --> pdb=" O SER b 182 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER b 182 " --> pdb=" O CYS b 139 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR b 178 " --> pdb=" O ASN b 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.525A pdb=" N ASN b 150 " --> pdb=" O THR b 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR b 197 " --> pdb=" O PHE b 214 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE b 214 " --> pdb=" O TYR b 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS b 199 " --> pdb=" O LYS b 212 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS b 212 " --> pdb=" O CYS b 199 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA b 201 " --> pdb=" O ILE b 210 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE b 210 " --> pdb=" O ALA b 201 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 393 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: 1.24 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1398 1.33 - 1.46: 1043 1.46 - 1.58: 2540 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 5007 Sorted by residual: bond pdb=" CA PHE A 490 " pdb=" C PHE A 490 " ideal model delta sigma weight residual 1.528 1.503 0.025 1.18e-02 7.18e+03 4.62e+00 bond pdb=" C ASN a 52 " pdb=" O ASN a 52 " ideal model delta sigma weight residual 1.241 1.213 0.027 1.33e-02 5.65e+03 4.22e+00 bond pdb=" CA GLN A 493 " pdb=" C GLN A 493 " ideal model delta sigma weight residual 1.528 1.497 0.031 1.51e-02 4.39e+03 4.11e+00 bond pdb=" CA ILE a 55 " pdb=" C ILE a 55 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.12e-02 7.97e+03 3.99e+00 bond pdb=" C LEU A 492 " pdb=" O LEU A 492 " ideal model delta sigma weight residual 1.235 1.214 0.021 1.18e-02 7.18e+03 3.18e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 100.65 - 107.31: 184 107.31 - 113.98: 2732 113.98 - 120.65: 1881 120.65 - 127.32: 1975 127.32 - 133.99: 53 Bond angle restraints: 6825 Sorted by residual: angle pdb=" C LYS a 65 " pdb=" N ASP a 66 " pdb=" CA ASP a 66 " ideal model delta sigma weight residual 122.08 129.13 -7.05 1.47e+00 4.63e-01 2.30e+01 angle pdb=" N TYR A 489 " pdb=" CA TYR A 489 " pdb=" C TYR A 489 " ideal model delta sigma weight residual 109.65 116.18 -6.53 1.56e+00 4.11e-01 1.75e+01 angle pdb=" C ARG b 113 " pdb=" N ALA b 114 " pdb=" CA ALA b 114 " ideal model delta sigma weight residual 121.70 129.21 -7.51 1.80e+00 3.09e-01 1.74e+01 angle pdb=" N ASP a 56 " pdb=" CA ASP a 56 " pdb=" C ASP a 56 " ideal model delta sigma weight residual 111.39 117.09 -5.70 1.38e+00 5.25e-01 1.71e+01 angle pdb=" C ILE a 51 " pdb=" CA ILE a 51 " pdb=" CB ILE a 51 " ideal model delta sigma weight residual 111.29 105.20 6.09 1.64e+00 3.72e-01 1.38e+01 ... (remaining 6820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 2652 15.46 - 30.93: 244 30.93 - 46.39: 59 46.39 - 61.85: 14 61.85 - 77.31: 7 Dihedral angle restraints: 2976 sinusoidal: 1136 harmonic: 1840 Sorted by residual: dihedral pdb=" CB CYS b 139 " pdb=" SG CYS b 139 " pdb=" SG CYS b 199 " pdb=" CB CYS b 199 " ideal model delta sinusoidal sigma weight residual 93.00 169.59 -76.59 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 16.61 76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CA GLY A 502 " pdb=" C GLY A 502 " pdb=" N VAL A 503 " pdb=" CA VAL A 503 " ideal model delta harmonic sigma weight residual -180.00 -138.94 -41.06 0 5.00e+00 4.00e-02 6.74e+01 ... (remaining 2973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 596 0.050 - 0.099: 118 0.099 - 0.149: 35 0.149 - 0.199: 5 0.199 - 0.248: 1 Chirality restraints: 755 Sorted by residual: chirality pdb=" CA ASP a 56 " pdb=" N ASP a 56 " pdb=" C ASP a 56 " pdb=" CB ASP a 56 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE b 155 " pdb=" CA ILE b 155 " pdb=" CG1 ILE b 155 " pdb=" CG2 ILE b 155 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA TYR A 489 " pdb=" N TYR A 489 " pdb=" C TYR A 489 " pdb=" CB TYR A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 752 not shown) Planarity restraints: 875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 502 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLY A 502 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY A 502 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 503 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU a 152 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO a 153 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO a 153 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO a 153 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 491 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.025 5.00e-02 4.00e+02 ... (remaining 872 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 5 2.35 - 2.99: 2317 2.99 - 3.63: 6348 3.63 - 4.26: 10307 4.26 - 4.90: 17217 Nonbonded interactions: 36194 Sorted by model distance: nonbonded pdb=" CD1 LEU A 455 " pdb=" OE1 GLN A 493 " model vdw 1.713 3.460 nonbonded pdb=" CD1 LEU A 455 " pdb=" CD GLN A 493 " model vdw 1.960 3.690 nonbonded pdb=" CD1 LEU A 455 " pdb=" NE2 GLN A 493 " model vdw 2.206 3.540 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.290 2.440 nonbonded pdb=" OD1 ASP b 88 " pdb=" OH TYR b 92 " model vdw 2.314 2.440 ... (remaining 36189 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: 3.760 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: 0.020 Extract box with map and model: 13.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.870 Find NCS groups from input model: 0.170 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 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 : 0.003 0.031 5007 Z= 0.197 Angle : 0.708 7.512 6825 Z= 0.420 Chirality : 0.046 0.248 755 Planarity : 0.006 0.046 875 Dihedral : 12.878 77.314 1776 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.73 % Favored : 96.95 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.76 (0.28), residues: 622 helix: -5.01 (0.15), residues: 42 sheet: -0.54 (0.32), residues: 223 loop : -2.37 (0.26), residues: 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 186 average time/residue: 0.1713 time to fit residues: 39.8544 Evaluate side-chains 139 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0571 time to fit residues: 1.2538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.0040 chunk 55 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 GLN b 34 ASN b 37 ASN ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 5007 Z= 0.226 Angle : 0.586 6.866 6825 Z= 0.303 Chirality : 0.043 0.196 755 Planarity : 0.005 0.056 875 Dihedral : 4.224 27.348 684 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -1.93 (0.30), residues: 622 helix: -4.28 (0.31), residues: 42 sheet: -0.11 (0.32), residues: 232 loop : -1.76 (0.29), residues: 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 147 average time/residue: 0.1567 time to fit residues: 29.6970 Evaluate side-chains 126 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0474 time to fit residues: 1.4802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 0.0020 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN a 6 GLN b 6 GLN b 43 GLN b 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5007 Z= 0.151 Angle : 0.544 7.129 6825 Z= 0.274 Chirality : 0.043 0.190 755 Planarity : 0.004 0.046 875 Dihedral : 4.048 22.032 684 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -1.47 (0.31), residues: 622 helix: -3.49 (0.53), residues: 42 sheet: 0.26 (0.33), residues: 232 loop : -1.57 (0.30), residues: 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 0.1508 time to fit residues: 25.7322 Evaluate side-chains 120 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.482 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0554 time to fit residues: 1.2284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 GLN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 5007 Z= 0.238 Angle : 0.591 9.046 6825 Z= 0.301 Chirality : 0.044 0.192 755 Planarity : 0.004 0.044 875 Dihedral : 4.271 22.098 684 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -1.07 (0.32), residues: 622 helix: -2.93 (0.67), residues: 42 sheet: 0.60 (0.33), residues: 237 loop : -1.42 (0.31), residues: 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.1407 time to fit residues: 24.4775 Evaluate side-chains 119 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0544 time to fit residues: 1.8487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 159 ASN a 168 HIS b 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 5007 Z= 0.286 Angle : 0.631 8.501 6825 Z= 0.322 Chirality : 0.044 0.173 755 Planarity : 0.004 0.042 875 Dihedral : 4.613 23.911 684 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.90 (0.33), residues: 622 helix: -2.43 (0.92), residues: 30 sheet: 0.61 (0.33), residues: 238 loop : -1.34 (0.31), residues: 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.582 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 119 average time/residue: 0.1501 time to fit residues: 23.5256 Evaluate side-chains 116 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0553 time to fit residues: 1.4642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 5007 Z= 0.218 Angle : 0.594 8.395 6825 Z= 0.300 Chirality : 0.044 0.166 755 Planarity : 0.004 0.040 875 Dihedral : 4.406 21.900 684 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.75 (0.33), residues: 622 helix: -2.35 (0.93), residues: 30 sheet: 0.77 (0.33), residues: 237 loop : -1.28 (0.32), residues: 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.620 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 119 average time/residue: 0.1520 time to fit residues: 24.0134 Evaluate side-chains 113 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0521 time to fit residues: 1.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.0070 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 17 optimal weight: 0.0370 chunk 11 optimal weight: 0.3980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5007 Z= 0.144 Angle : 0.549 9.391 6825 Z= 0.275 Chirality : 0.043 0.172 755 Planarity : 0.004 0.038 875 Dihedral : 4.091 20.145 684 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.75 (0.33), residues: 622 helix: -2.40 (0.82), residues: 36 sheet: 0.77 (0.33), residues: 238 loop : -1.25 (0.33), residues: 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 0.580 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 125 average time/residue: 0.1433 time to fit residues: 23.7717 Evaluate side-chains 118 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0553 time to fit residues: 1.0716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.0170 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5007 Z= 0.196 Angle : 0.595 11.202 6825 Z= 0.293 Chirality : 0.044 0.173 755 Planarity : 0.004 0.036 875 Dihedral : 4.202 21.203 684 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.34), residues: 622 helix: -2.33 (0.93), residues: 30 sheet: 0.85 (0.33), residues: 237 loop : -1.17 (0.33), residues: 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 120 average time/residue: 0.1462 time to fit residues: 23.2836 Evaluate side-chains 114 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0512 time to fit residues: 1.2454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 5007 Z= 0.234 Angle : 0.620 10.585 6825 Z= 0.309 Chirality : 0.044 0.135 755 Planarity : 0.004 0.036 875 Dihedral : 4.410 22.347 684 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.68 (0.33), residues: 622 helix: -2.37 (0.91), residues: 30 sheet: 0.99 (0.35), residues: 220 loop : -1.25 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.1678 time to fit residues: 24.8105 Evaluate side-chains 107 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0740 time to fit residues: 0.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5007 Z= 0.184 Angle : 0.603 10.935 6825 Z= 0.299 Chirality : 0.043 0.135 755 Planarity : 0.004 0.035 875 Dihedral : 4.296 20.745 684 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.33), residues: 622 helix: -2.39 (0.92), residues: 30 sheet: 0.85 (0.33), residues: 232 loop : -1.20 (0.32), residues: 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.1568 time to fit residues: 23.4186 Evaluate side-chains 106 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0528 time to fit residues: 0.6974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.0000 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.196020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174933 restraints weight = 8625.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.178928 restraints weight = 5309.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.181664 restraints weight = 3734.737| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5007 Z= 0.191 Angle : 0.596 10.241 6825 Z= 0.298 Chirality : 0.044 0.136 755 Planarity : 0.004 0.036 875 Dihedral : 4.274 21.079 684 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.33), residues: 622 helix: -2.41 (0.91), residues: 30 sheet: 0.83 (0.33), residues: 238 loop : -1.14 (0.32), residues: 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1565.85 seconds wall clock time: 28 minutes 48.57 seconds (1728.57 seconds total)