Starting phenix.real_space_refine on Sat Dec 28 21:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzj_27801/12_2024/8dzj_27801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzj_27801/12_2024/8dzj_27801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/12_2024/8dzj_27801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzj_27801/12_2024/8dzj_27801.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzj_27801/12_2024/8dzj_27801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzj_27801/12_2024/8dzj_27801.cif" } resolution = 2.9 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= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 190 5.49 5 S 21 5.16 5 C 4988 2.51 5 N 1635 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9030 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3369 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1622 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3272 Classifications: {'RNA': 153} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 75, 'rna3p_pyr': 62} Link IDs: {'rna2p': 16, 'rna3p': 136} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2994 SG CYS A 372 44.439 13.422 45.939 1.00 30.07 S ATOM 3015 SG CYS A 375 42.544 10.078 46.726 1.00 35.03 S ATOM 3132 SG CYS A 391 45.670 10.363 47.236 1.00 37.27 S ATOM 3154 SG CYS A 394 44.416 9.788 43.268 1.00 37.08 S Time building chain proxies: 6.26, per 1000 atoms: 0.69 Number of scatterers: 9030 At special positions: 0 Unit cell: (85.2, 116.085, 137.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 190 15.00 O 2195 8.00 N 1635 7.00 C 4988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.58 Conformation dependent library (CDL) restraints added in 674.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 391 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 375 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 372 " Number of angles added : 6 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 50.6% alpha, 20.1% beta 69 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 16 through 57 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.736A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.517A pdb=" N TYR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 170 through 182 Processing helix chain 'A' and resid 247 through 270 removed outlier: 3.814A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.141A pdb=" N HIS A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 316 Processing helix chain 'A' and resid 325 through 330 removed outlier: 4.120A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'A' and resid 400 through 410 Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'B' and resid 16 through 46 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.525A pdb=" N TYR B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 111 removed outlier: 5.481A pdb=" N LYS B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 171 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 4.550A pdb=" N SER A 206 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 190 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 204 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 192 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 202 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HIS A 194 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS A 200 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP A 201 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 9 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 168 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 11 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 164 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.034A pdb=" N MET A 222 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU A 324 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ILE A 224 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 321 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE A 363 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET A 323 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 5.064A pdb=" N TRP B 201 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 11 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR B 142 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 295 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 174 hydrogen bonds 324 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.95 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: 1711 1.33 - 1.45: 3255 1.45 - 1.57: 4226 1.57 - 1.69: 376 1.69 - 1.81: 37 Bond restraints: 9605 Sorted by residual: bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.61e+00 bond pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.65e+00 bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.03e+00 bond pdb=" N VAL A 257 " pdb=" CA VAL A 257 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.30e-02 5.92e+03 7.77e+00 bond pdb=" N GLU A 251 " pdb=" CA GLU A 251 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.70e+00 ... (remaining 9600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13336 1.41 - 2.81: 448 2.81 - 4.22: 65 4.22 - 5.63: 13 5.63 - 7.04: 2 Bond angle restraints: 13864 Sorted by residual: angle pdb=" C ARG A 280 " pdb=" N ASP A 281 " pdb=" CA ASP A 281 " ideal model delta sigma weight residual 121.54 128.58 -7.04 1.91e+00 2.74e-01 1.36e+01 angle pdb=" CA ILE A 250 " pdb=" C ILE A 250 " pdb=" O ILE A 250 " ideal model delta sigma weight residual 121.17 117.40 3.77 1.06e+00 8.90e-01 1.27e+01 angle pdb=" CA ILE A 332 " pdb=" C ILE A 332 " pdb=" O ILE A 332 " ideal model delta sigma weight residual 120.96 117.30 3.66 1.19e+00 7.06e-01 9.46e+00 angle pdb=" CA GLN A 256 " pdb=" C GLN A 256 " pdb=" O GLN A 256 " ideal model delta sigma weight residual 120.82 117.79 3.03 1.05e+00 9.07e-01 8.35e+00 angle pdb=" CA ASP A 331 " pdb=" C ASP A 331 " pdb=" O ASP A 331 " ideal model delta sigma weight residual 120.82 117.80 3.02 1.05e+00 9.07e-01 8.26e+00 ... (remaining 13859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 4904 21.54 - 43.09: 522 43.09 - 64.63: 356 64.63 - 86.17: 45 86.17 - 107.71: 6 Dihedral angle restraints: 5833 sinusoidal: 4038 harmonic: 1795 Sorted by residual: dihedral pdb=" CA LYS A 282 " pdb=" C LYS A 282 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " ideal model delta harmonic sigma weight residual 180.00 -158.50 -21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" O4' C E 94 " pdb=" C1' C E 94 " pdb=" N1 C E 94 " pdb=" C2 C E 94 " ideal model delta sinusoidal sigma weight residual -128.00 -65.32 -62.68 1 1.70e+01 3.46e-03 1.80e+01 dihedral pdb=" O4' A E 106 " pdb=" C1' A E 106 " pdb=" N9 A E 106 " pdb=" C4 A E 106 " ideal model delta sinusoidal sigma weight residual -78.00 -16.27 -61.73 1 1.70e+01 3.46e-03 1.75e+01 ... (remaining 5830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1465 0.060 - 0.119: 149 0.119 - 0.179: 25 0.179 - 0.239: 2 0.239 - 0.298: 1 Chirality restraints: 1642 Sorted by residual: chirality pdb=" P G E 34 " pdb=" OP1 G E 34 " pdb=" OP2 G E 34 " pdb=" O5' G E 34 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA LEU A 337 " pdb=" N LEU A 337 " pdb=" C LEU A 337 " pdb=" CB LEU A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1' A E 91 " pdb=" O4' A E 91 " pdb=" C2' A E 91 " pdb=" N9 A E 91 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 1639 not shown) Planarity restraints: 1064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 233 " 0.015 2.00e-02 2.50e+03 1.53e-02 4.67e+00 pdb=" CG TYR A 233 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 233 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 233 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 233 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 233 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 233 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 233 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E 31 " -0.026 2.00e-02 2.50e+03 1.20e-02 4.30e+00 pdb=" N9 G E 31 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G E 31 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G E 31 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G E 31 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G E 31 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G E 31 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G E 31 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G E 31 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G E 31 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G E 31 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G E 31 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 91 " 0.026 2.00e-02 2.50e+03 1.12e-02 3.48e+00 pdb=" N9 A E 91 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A E 91 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A E 91 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A E 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A E 91 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A E 91 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A E 91 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A E 91 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A E 91 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A E 91 " -0.005 2.00e-02 2.50e+03 ... (remaining 1061 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1068 2.75 - 3.29: 8440 3.29 - 3.82: 17829 3.82 - 4.36: 21444 4.36 - 4.90: 31208 Nonbonded interactions: 79989 Sorted by model distance: nonbonded pdb=" OE1 GLU A 288 " pdb=" NH2 ARG A 291 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG A 291 " pdb=" OP1 DC C 21 " model vdw 2.211 3.120 nonbonded pdb=" O6 G E 36 " pdb=" O4 U E 62 " model vdw 2.229 2.432 nonbonded pdb=" O2' C E 174 " pdb=" O4' U E 175 " model vdw 2.235 3.040 nonbonded pdb=" O TYR B 84 " pdb=" OG SER B 150 " model vdw 2.255 3.040 ... (remaining 79984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.310 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9605 Z= 0.220 Angle : 0.604 7.037 13864 Z= 0.359 Chirality : 0.039 0.298 1642 Planarity : 0.004 0.038 1064 Dihedral : 21.353 107.713 4685 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.38 % Allowed : 0.19 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.33), residues: 605 helix: 1.65 (0.30), residues: 298 sheet: 0.21 (0.43), residues: 130 loop : -0.75 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 43 HIS 0.012 0.001 HIS A 303 PHE 0.008 0.001 PHE A 336 TYR 0.036 0.002 TYR A 233 ARG 0.012 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 1.3240 time to fit residues: 125.3269 Evaluate side-chains 47 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9605 Z= 0.177 Angle : 0.549 6.546 13864 Z= 0.296 Chirality : 0.035 0.189 1642 Planarity : 0.005 0.040 1064 Dihedral : 22.491 106.258 3433 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.32 % Allowed : 9.42 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.33), residues: 605 helix: 2.28 (0.29), residues: 304 sheet: 0.19 (0.41), residues: 134 loop : -0.74 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 45 HIS 0.006 0.001 HIS A 303 PHE 0.008 0.001 PHE A 389 TYR 0.024 0.001 TYR A 351 ARG 0.011 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.758 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 1.1477 time to fit residues: 67.2718 Evaluate side-chains 46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 346 GLN A 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9605 Z= 0.383 Angle : 0.668 9.900 13864 Z= 0.355 Chirality : 0.041 0.272 1642 Planarity : 0.005 0.051 1064 Dihedral : 22.701 105.233 3433 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.07 % Allowed : 10.55 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.33), residues: 605 helix: 2.09 (0.29), residues: 304 sheet: -0.05 (0.40), residues: 132 loop : -0.85 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 43 HIS 0.009 0.002 HIS A 303 PHE 0.011 0.002 PHE A 253 TYR 0.023 0.002 TYR A 351 ARG 0.007 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.840 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 53 average time/residue: 1.3012 time to fit residues: 74.2618 Evaluate side-chains 39 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9605 Z= 0.168 Angle : 0.557 8.726 13864 Z= 0.299 Chirality : 0.035 0.203 1642 Planarity : 0.004 0.041 1064 Dihedral : 22.388 109.285 3431 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.69 % Allowed : 12.43 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.34), residues: 605 helix: 2.33 (0.29), residues: 304 sheet: 0.14 (0.41), residues: 134 loop : -0.66 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 45 HIS 0.004 0.001 HIS A 303 PHE 0.019 0.002 PHE A 253 TYR 0.021 0.001 TYR A 351 ARG 0.005 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.697 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 1.0844 time to fit residues: 58.9655 Evaluate side-chains 41 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 9605 Z= 0.471 Angle : 0.721 9.555 13864 Z= 0.384 Chirality : 0.044 0.306 1642 Planarity : 0.005 0.055 1064 Dihedral : 22.725 105.053 3431 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.94 % Allowed : 14.69 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.33), residues: 605 helix: 1.89 (0.29), residues: 302 sheet: -0.08 (0.41), residues: 130 loop : -0.96 (0.43), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 43 HIS 0.006 0.002 HIS A 303 PHE 0.019 0.002 PHE A 253 TYR 0.022 0.003 TYR A 270 ARG 0.007 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 1.4550 time to fit residues: 63.7629 Evaluate side-chains 40 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9605 Z= 0.178 Angle : 0.570 14.493 13864 Z= 0.303 Chirality : 0.035 0.200 1642 Planarity : 0.004 0.040 1064 Dihedral : 22.358 109.906 3431 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.51 % Allowed : 14.50 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.34), residues: 605 helix: 2.30 (0.30), residues: 303 sheet: -0.07 (0.41), residues: 132 loop : -0.62 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 45 HIS 0.003 0.001 HIS A 278 PHE 0.026 0.002 PHE A 253 TYR 0.021 0.001 TYR A 351 ARG 0.005 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 1.1403 time to fit residues: 56.8824 Evaluate side-chains 44 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 191 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9605 Z= 0.186 Angle : 0.575 14.106 13864 Z= 0.306 Chirality : 0.035 0.189 1642 Planarity : 0.004 0.040 1064 Dihedral : 22.327 108.088 3431 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.07 % Allowed : 15.44 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.34), residues: 605 helix: 2.36 (0.30), residues: 303 sheet: -0.02 (0.42), residues: 131 loop : -0.59 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 45 HIS 0.003 0.001 HIS A 278 PHE 0.031 0.002 PHE A 253 TYR 0.024 0.001 TYR A 270 ARG 0.005 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 1.2094 time to fit residues: 65.6824 Evaluate side-chains 46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 191 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9605 Z= 0.176 Angle : 0.587 12.836 13864 Z= 0.310 Chirality : 0.035 0.185 1642 Planarity : 0.004 0.041 1064 Dihedral : 22.294 107.512 3431 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.69 % Allowed : 15.82 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.34), residues: 605 helix: 2.32 (0.30), residues: 302 sheet: 0.02 (0.42), residues: 132 loop : -0.59 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 45 HIS 0.003 0.001 HIS A 278 PHE 0.037 0.002 PHE A 253 TYR 0.027 0.001 TYR A 270 ARG 0.004 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 1.2557 time to fit residues: 63.8239 Evaluate side-chains 46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 191 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9605 Z= 0.244 Angle : 0.628 12.869 13864 Z= 0.328 Chirality : 0.036 0.183 1642 Planarity : 0.004 0.039 1064 Dihedral : 22.321 106.318 3431 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.69 % Allowed : 16.01 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.34), residues: 605 helix: 2.28 (0.30), residues: 302 sheet: -0.02 (0.42), residues: 131 loop : -0.65 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 43 HIS 0.003 0.001 HIS A 278 PHE 0.046 0.002 PHE A 253 TYR 0.021 0.002 TYR A 270 ARG 0.004 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 1.2027 time to fit residues: 58.5478 Evaluate side-chains 46 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 191 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9605 Z= 0.224 Angle : 0.623 13.075 13864 Z= 0.328 Chirality : 0.036 0.184 1642 Planarity : 0.004 0.039 1064 Dihedral : 22.280 106.820 3431 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.51 % Allowed : 16.95 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.34), residues: 605 helix: 2.24 (0.30), residues: 302 sheet: -0.07 (0.42), residues: 132 loop : -0.60 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 45 HIS 0.003 0.001 HIS A 278 PHE 0.052 0.003 PHE A 253 TYR 0.019 0.001 TYR A 351 ARG 0.003 0.000 ARG A 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 45 average time/residue: 1.2141 time to fit residues: 59.1540 Evaluate side-chains 48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 191 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.0370 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** 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 = 0.3979 r_free = 0.3979 target = 0.088018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.062695 restraints weight = 27314.848| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.31 r_work: 0.3216 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9605 Z= 0.219 Angle : 0.621 13.070 13864 Z= 0.325 Chirality : 0.035 0.182 1642 Planarity : 0.004 0.039 1064 Dihedral : 22.266 106.941 3431 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.51 % Allowed : 16.76 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.34), residues: 605 helix: 2.25 (0.30), residues: 302 sheet: -0.11 (0.42), residues: 132 loop : -0.62 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 45 HIS 0.003 0.001 HIS A 278 PHE 0.054 0.003 PHE A 253 TYR 0.023 0.001 TYR A 308 ARG 0.003 0.000 ARG B 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2409.50 seconds wall clock time: 44 minutes 49.92 seconds (2689.92 seconds total)