Starting phenix.real_space_refine on Wed Jan 17 16:59:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/01_2024/7wcr_32428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/01_2024/7wcr_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_32428/01_2024/7wcr_32428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/01_2024/7wcr_32428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/01_2024/7wcr_32428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcr_32428/01_2024/7wcr_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-1.21-5211/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: 3.12, 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: 1.66 Conformation dependent library (CDL) restraints added in 920.2 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: 1.88 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: 3.060 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: 13.180 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- 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 % Allowed : 5.65 % Favored : 93.08 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.011 0.001 PHE b 144 TYR 0.010 0.001 TYR A 501 ARG 0.001 0.000 ARG b 18 *********************** 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 : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.7911 (mp) cc_final: 0.7528 (pt) REVERT: b 42 TYR cc_start: 0.7893 (m-80) cc_final: 0.7493 (m-80) outliers start: 7 outliers final: 5 residues processed: 186 average time/residue: 0.1743 time to fit residues: 40.4299 Evaluate side-chains 140 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain a residue 52 ASN Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 59 THR 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: 0.7980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 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: 0.6992 ------------------------------------------------------------------------------- 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: 0.6623 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5007 Z= 0.246 Angle : 0.595 6.580 6825 Z= 0.313 Chirality : 0.043 0.176 755 Planarity : 0.005 0.055 875 Dihedral : 5.286 51.530 694 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.46 % Allowed : 16.21 % Favored : 80.33 % 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: -4.26 (0.31), residues: 42 sheet: -0.11 (0.32), residues: 235 loop : -1.77 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 36 HIS 0.007 0.001 HIS b 203 PHE 0.019 0.002 PHE b 77 TYR 0.016 0.002 TYR a 179 ARG 0.004 0.001 ARG b 113 *********************** 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 163 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8081 (p90) cc_final: 0.7559 (p90) REVERT: A 448 ASN cc_start: 0.6280 (t0) cc_final: 0.5959 (m-40) REVERT: A 468 ILE cc_start: 0.8118 (mp) cc_final: 0.7884 (mp) REVERT: a 10 GLU cc_start: 0.7086 (mp0) cc_final: 0.6806 (mp0) REVERT: a 19 LYS cc_start: 0.7440 (mttt) cc_final: 0.6971 (pttm) REVERT: a 195 GLU cc_start: 0.6286 (tp30) cc_final: 0.5892 (mt-10) REVERT: b 4 MET cc_start: 0.6584 (mtt) cc_final: 0.6180 (mtt) outliers start: 19 outliers final: 13 residues processed: 152 average time/residue: 0.1510 time to fit residues: 29.6646 Evaluate side-chains 136 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 183 SER Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.0470 overall best weight: 0.2302 ------------------------------------------------------------------------------- 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 6 GLN a 43 GLN a 62 GLN b 6 GLN b 34 ASN b 43 GLN b 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5007 Z= 0.157 Angle : 0.533 6.448 6825 Z= 0.272 Chirality : 0.043 0.201 755 Planarity : 0.004 0.045 875 Dihedral : 4.653 49.713 688 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.73 % Allowed : 20.95 % Favored : 76.32 % 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: -1.46 (0.31), residues: 622 helix: -3.47 (0.54), residues: 42 sheet: 0.25 (0.33), residues: 234 loop : -1.56 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS b 203 PHE 0.019 0.001 PHE b 77 TYR 0.016 0.001 TYR A 449 ARG 0.009 0.001 ARG b 60 *********************** 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 138 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 ASP cc_start: 0.7251 (m-30) cc_final: 0.6991 (m-30) REVERT: A 448 ASN cc_start: 0.6307 (t0) cc_final: 0.5657 (m-40) REVERT: A 468 ILE cc_start: 0.8075 (mp) cc_final: 0.7810 (mp) REVERT: a 19 LYS cc_start: 0.7341 (mttt) cc_final: 0.6964 (pttm) REVERT: b 42 TYR cc_start: 0.8092 (m-80) cc_final: 0.7771 (m-80) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.1503 time to fit residues: 25.4421 Evaluate side-chains 130 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3994 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= 0.229 Angle : 0.577 7.174 6825 Z= 0.297 Chirality : 0.043 0.191 755 Planarity : 0.004 0.046 875 Dihedral : 4.947 48.241 688 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.37 % Allowed : 20.58 % Favored : 75.05 % 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: -1.00 (0.32), residues: 622 helix: -2.87 (0.77), residues: 36 sheet: 0.54 (0.33), residues: 236 loop : -1.31 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 153 HIS 0.005 0.001 HIS a 203 PHE 0.018 0.002 PHE b 77 TYR 0.020 0.002 TYR b 97 ARG 0.003 0.000 ARG b 113 *********************** 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 151 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.6742 (mt) cc_final: 0.5891 (mp) REVERT: A 468 ILE cc_start: 0.8159 (mp) cc_final: 0.7907 (mp) REVERT: a 19 LYS cc_start: 0.7486 (mttt) cc_final: 0.7113 (pttm) outliers start: 24 outliers final: 20 residues processed: 140 average time/residue: 0.1407 time to fit residues: 25.8934 Evaluate side-chains 134 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 151 VAL Chi-restraints excluded: chain b residue 175 ASP Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 159 ASN b 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5007 Z= 0.241 Angle : 0.604 8.711 6825 Z= 0.305 Chirality : 0.043 0.169 755 Planarity : 0.004 0.043 875 Dihedral : 5.157 47.989 688 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.37 % Allowed : 22.59 % Favored : 73.04 % 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: -0.76 (0.33), residues: 622 helix: -2.24 (1.00), residues: 30 sheet: 0.63 (0.33), residues: 237 loop : -1.18 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 158 HIS 0.002 0.001 HIS a 168 PHE 0.018 0.002 PHE A 338 TYR 0.016 0.002 TYR b 97 ARG 0.003 0.001 ARG A 403 *********************** 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 146 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.7928 (tt) cc_final: 0.7595 (mm) REVERT: A 458 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7209 (mmtm) REVERT: A 468 ILE cc_start: 0.8062 (mp) cc_final: 0.7842 (mp) REVERT: a 19 LYS cc_start: 0.7273 (mttt) cc_final: 0.7065 (pttm) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.1462 time to fit residues: 25.6638 Evaluate side-chains 133 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 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: 0.6927 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 5007 Z= 0.383 Angle : 0.709 8.188 6825 Z= 0.366 Chirality : 0.046 0.197 755 Planarity : 0.005 0.038 875 Dihedral : 5.992 55.588 688 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.46 % Allowed : 22.04 % Favored : 72.50 % 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: -0.99 (0.33), residues: 622 helix: -2.26 (0.97), residues: 30 sheet: 0.43 (0.34), residues: 236 loop : -1.32 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 153 HIS 0.003 0.001 HIS A 519 PHE 0.018 0.002 PHE a 104 TYR 0.019 0.002 TYR b 97 ARG 0.003 0.001 ARG A 509 *********************** 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 152 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8259 (tt) cc_final: 0.7940 (tp) REVERT: A 458 LYS cc_start: 0.8526 (ptmt) cc_final: 0.7612 (mmmt) REVERT: A 468 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 474 GLN cc_start: 0.7194 (mt0) cc_final: 0.6925 (mt0) REVERT: a 19 LYS cc_start: 0.7484 (mttt) cc_final: 0.7197 (pttm) REVERT: a 109 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7238 (tp40) REVERT: b 210 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8034 (tp) outliers start: 30 outliers final: 24 residues processed: 137 average time/residue: 0.1435 time to fit residues: 25.8411 Evaluate side-chains 146 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5007 Z= 0.210 Angle : 0.613 7.920 6825 Z= 0.311 Chirality : 0.044 0.167 755 Planarity : 0.004 0.034 875 Dihedral : 5.610 58.823 688 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.01 % Allowed : 24.77 % Favored : 71.22 % 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: -0.85 (0.33), residues: 622 helix: -2.24 (0.97), residues: 30 sheet: 0.73 (0.33), residues: 226 loop : -1.32 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 158 HIS 0.003 0.001 HIS a 203 PHE 0.015 0.002 PHE b 77 TYR 0.016 0.002 TYR A 451 ARG 0.002 0.000 ARG b 113 *********************** 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 143 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6234 (m-80) cc_final: 0.5972 (m-10) REVERT: A 441 LEU cc_start: 0.8205 (tt) cc_final: 0.7912 (tp) REVERT: A 455 LEU cc_start: 0.7489 (mm) cc_final: 0.7252 (mm) REVERT: A 458 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7291 (mmmt) REVERT: A 468 ILE cc_start: 0.8149 (mp) cc_final: 0.7881 (mp) REVERT: A 474 GLN cc_start: 0.7170 (mt0) cc_final: 0.6926 (mt0) REVERT: a 19 LYS cc_start: 0.7519 (mttt) cc_final: 0.7214 (pttm) REVERT: a 62 GLN cc_start: 0.7280 (mm-40) cc_final: 0.7035 (mt0) REVERT: b 119 THR cc_start: 0.6349 (OUTLIER) cc_final: 0.6133 (p) REVERT: b 210 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7992 (tp) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 0.1469 time to fit residues: 25.6185 Evaluate side-chains 132 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5007 Z= 0.252 Angle : 0.646 12.029 6825 Z= 0.325 Chirality : 0.044 0.173 755 Planarity : 0.004 0.034 875 Dihedral : 5.435 49.126 688 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.65 % Allowed : 24.04 % Favored : 70.31 % 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: -0.87 (0.33), residues: 622 helix: -2.68 (0.79), residues: 36 sheet: 0.76 (0.33), residues: 225 loop : -1.29 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 153 HIS 0.002 0.001 HIS a 203 PHE 0.017 0.002 PHE b 77 TYR 0.020 0.002 TYR A 451 ARG 0.002 0.000 ARG a 98 *********************** 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 143 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6408 (m-80) cc_final: 0.6161 (m-10) REVERT: A 441 LEU cc_start: 0.8259 (tt) cc_final: 0.8018 (tp) REVERT: A 458 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7263 (mmmt) REVERT: A 468 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 474 GLN cc_start: 0.7360 (mt0) cc_final: 0.7087 (mt0) REVERT: a 19 LYS cc_start: 0.7537 (mttt) cc_final: 0.7230 (pttm) REVERT: a 178 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7019 (mt) REVERT: b 210 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7956 (tp) outliers start: 31 outliers final: 25 residues processed: 132 average time/residue: 0.1455 time to fit residues: 25.1634 Evaluate side-chains 139 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 180 MET Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 57 optimal weight: 0.0670 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5007 Z= 0.155 Angle : 0.598 11.711 6825 Z= 0.296 Chirality : 0.043 0.164 755 Planarity : 0.004 0.035 875 Dihedral : 4.866 49.347 688 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.46 % Allowed : 26.23 % Favored : 70.31 % 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: -0.79 (0.33), residues: 622 helix: -2.37 (0.93), residues: 30 sheet: 0.78 (0.34), residues: 222 loop : -1.24 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 158 HIS 0.003 0.001 HIS a 203 PHE 0.015 0.001 PHE b 77 TYR 0.011 0.001 TYR A 451 ARG 0.001 0.000 ARG b 113 *********************** 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 136 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6357 (m-80) cc_final: 0.6069 (m-10) REVERT: A 451 TYR cc_start: 0.7942 (m-80) cc_final: 0.7690 (m-10) REVERT: A 458 LYS cc_start: 0.8133 (ptmt) cc_final: 0.7244 (mmmt) REVERT: A 468 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7814 (mp) REVERT: a 19 LYS cc_start: 0.7365 (mttt) cc_final: 0.7082 (pttm) REVERT: a 109 GLN cc_start: 0.7950 (tp40) cc_final: 0.7502 (tp-100) REVERT: a 178 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6958 (mt) REVERT: a 195 GLU cc_start: 0.6593 (tp30) cc_final: 0.6356 (tm-30) REVERT: b 210 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7962 (tp) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.1545 time to fit residues: 25.5553 Evaluate side-chains 124 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 519 HIS a 62 GLN a 168 HIS b 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 5007 Z= 0.316 Angle : 0.675 11.792 6825 Z= 0.341 Chirality : 0.045 0.174 755 Planarity : 0.004 0.039 875 Dihedral : 5.126 48.162 686 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.01 % Allowed : 26.78 % Favored : 69.22 % 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: -0.81 (0.33), residues: 622 helix: -2.68 (0.79), residues: 36 sheet: 0.84 (0.34), residues: 217 loop : -1.22 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 153 HIS 0.002 0.001 HIS a 168 PHE 0.017 0.002 PHE b 77 TYR 0.014 0.002 TYR A 451 ARG 0.003 0.001 ARG A 454 ********************** 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 136 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6697 (m-80) cc_final: 0.6413 (m-10) REVERT: A 458 LYS cc_start: 0.8260 (ptmt) cc_final: 0.7354 (mmmt) REVERT: A 468 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7928 (mp) REVERT: a 19 LYS cc_start: 0.7487 (mttt) cc_final: 0.7222 (pttm) REVERT: a 109 GLN cc_start: 0.8008 (tp40) cc_final: 0.7551 (tp-100) REVERT: a 178 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7026 (mt) REVERT: a 200 ASN cc_start: 0.6287 (OUTLIER) cc_final: 0.5772 (m-40) REVERT: b 175 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: b 210 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8012 (tp) outliers start: 22 outliers final: 15 residues processed: 125 average time/residue: 0.1435 time to fit residues: 23.5460 Evaluate side-chains 132 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 54 ASN Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 200 ASN Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 175 ASP Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.194454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.172372 restraints weight = 8490.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.176597 restraints weight = 5104.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.179496 restraints weight = 3522.938| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5007 Z= 0.180 Angle : 0.610 11.456 6825 Z= 0.303 Chirality : 0.044 0.168 755 Planarity : 0.004 0.037 875 Dihedral : 4.861 49.016 686 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.28 % Allowed : 26.96 % Favored : 69.76 % 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: -0.78 (0.33), residues: 622 helix: -2.33 (0.96), residues: 29 sheet: 0.75 (0.33), residues: 224 loop : -1.23 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 158 HIS 0.003 0.001 HIS a 203 PHE 0.015 0.001 PHE b 77 TYR 0.011 0.001 TYR A 505 ARG 0.002 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.62 seconds wall clock time: 29 minutes 20.14 seconds (1760.14 seconds total)