Starting phenix.real_space_refine on Thu Nov 14 19:03:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaz_35323/11_2024/8iaz_35323.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaz_35323/11_2024/8iaz_35323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaz_35323/11_2024/8iaz_35323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaz_35323/11_2024/8iaz_35323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaz_35323/11_2024/8iaz_35323.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaz_35323/11_2024/8iaz_35323.cif" } resolution = 3.0 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= 0.012 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 203 5.49 5 S 16 5.16 5 C 3919 2.51 5 N 1333 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7396 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3110 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 374} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3464 Classifications: {'RNA': 163} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 10, 'rna3p_pur': 74, 'rna3p_pyr': 61} Link IDs: {'rna2p': 22, 'rna3p': 140} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 490 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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 2769 SG CYS A 343 12.251 39.929 54.366 0.35 19.85 S ATOM 2791 SG CYS A 346 9.833 37.189 55.351 0.14 23.35 S ATOM 2917 SG CYS A 362 11.328 37.075 51.877 0.33 19.10 S ATOM 2929 SG CYS A 364 8.759 39.462 52.559 0.16 24.39 S Time building chain proxies: 5.17, per 1000 atoms: 0.70 Number of scatterers: 7396 At special positions: 0 Unit cell: (98.04, 123.84, 98.9, 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 16 16.00 P 203 15.00 O 1924 8.00 N 1333 7.00 C 3919 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: 2.08 Conformation dependent library (CDL) restraints added in 422.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 362 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 346 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 364 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 343 " Number of angles added : 6 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 3 sheets defined 47.4% alpha, 12.0% beta 52 base pairs and 111 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 15 through 47 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.657A pdb=" N VAL A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.670A pdb=" N VAL A 77 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.717A pdb=" N VAL A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 215 through 242 removed outlier: 3.751A pdb=" N ARG A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 282 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.614A pdb=" N MET A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.710A pdb=" N LYS A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 Processing helix chain 'A' and resid 370 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.309A pdb=" N SER A 160 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR A 170 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 174 " --> pdb=" O PHE A 8 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 142 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.155A pdb=" N ILE A 287 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 332 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 361 154 hydrogen bonds defined for protein. 435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 111 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 817 1.32 - 1.44: 3287 1.44 - 1.56: 3440 1.56 - 1.69: 396 1.69 - 1.81: 22 Bond restraints: 7962 Sorted by residual: bond pdb=" O3' C E 196 " pdb=" P C E 197 " ideal model delta sigma weight residual 1.607 1.432 0.175 1.50e-02 4.44e+03 1.36e+02 bond pdb=" P C E 196 " pdb=" OP2 C E 196 " ideal model delta sigma weight residual 1.485 1.363 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" P C E 197 " pdb=" OP2 C E 197 " ideal model delta sigma weight residual 1.485 1.392 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C3' C E 196 " pdb=" O3' C E 196 " ideal model delta sigma weight residual 1.417 1.350 0.067 1.50e-02 4.44e+03 1.97e+01 bond pdb=" P C E 196 " pdb=" OP1 C E 196 " ideal model delta sigma weight residual 1.485 1.398 0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 7957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 11604 3.86 - 7.73: 60 7.73 - 11.59: 9 11.59 - 15.45: 0 15.45 - 19.32: 1 Bond angle restraints: 11674 Sorted by residual: angle pdb=" O2' C E 197 " pdb=" C2' C E 197 " pdb=" C1' C E 197 " ideal model delta sigma weight residual 108.40 89.08 19.32 1.50e+00 4.44e-01 1.66e+02 angle pdb=" O2' A E 198 " pdb=" C2' A E 198 " pdb=" C1' A E 198 " ideal model delta sigma weight residual 108.40 97.97 10.43 1.50e+00 4.44e-01 4.84e+01 angle pdb=" C3' A E 198 " pdb=" C2' A E 198 " pdb=" O2' A E 198 " ideal model delta sigma weight residual 110.70 100.37 10.33 1.50e+00 4.44e-01 4.74e+01 angle pdb=" C2' C E 197 " pdb=" C1' C E 197 " pdb=" N1 C E 197 " ideal model delta sigma weight residual 112.00 120.95 -8.95 1.50e+00 4.44e-01 3.56e+01 angle pdb=" C2' DG C 4 " pdb=" C1' DG C 4 " pdb=" N9 DG C 4 " ideal model delta sigma weight residual 113.50 121.84 -8.34 1.50e+00 4.44e-01 3.09e+01 ... (remaining 11669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 4227 35.58 - 71.16: 592 71.16 - 106.74: 32 106.74 - 142.32: 6 142.32 - 177.89: 15 Dihedral angle restraints: 4872 sinusoidal: 3740 harmonic: 1132 Sorted by residual: dihedral pdb=" O4' U E 189 " pdb=" C1' U E 189 " pdb=" N1 U E 189 " pdb=" C2 U E 189 " ideal model delta sinusoidal sigma weight residual -160.00 17.31 -177.31 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 82 " pdb=" C1' U E 82 " pdb=" N1 U E 82 " pdb=" C2 U E 82 " ideal model delta sinusoidal sigma weight residual -160.00 16.45 -176.45 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 134 " pdb=" C1' U E 134 " pdb=" N1 U E 134 " pdb=" C2 U E 134 " ideal model delta sinusoidal sigma weight residual -160.00 7.65 -167.65 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 4869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1288 0.070 - 0.140: 113 0.140 - 0.210: 18 0.210 - 0.279: 6 0.279 - 0.349: 3 Chirality restraints: 1428 Sorted by residual: chirality pdb=" P C E 196 " pdb=" OP1 C E 196 " pdb=" OP2 C E 196 " pdb=" O5' C E 196 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" P C E 197 " pdb=" OP1 C E 197 " pdb=" OP2 C E 197 " pdb=" O5' C E 197 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C1' C E 197 " pdb=" O4' C E 197 " pdb=" C2' C E 197 " pdb=" N1 C E 197 " both_signs ideal model delta sigma weight residual False 2.47 2.14 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1425 not shown) Planarity restraints: 736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C E 196 " 0.066 2.00e-02 2.50e+03 3.51e-02 2.78e+01 pdb=" N1 C E 196 " -0.047 2.00e-02 2.50e+03 pdb=" C2 C E 196 " -0.036 2.00e-02 2.50e+03 pdb=" O2 C E 196 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C E 196 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C E 196 " -0.022 2.00e-02 2.50e+03 pdb=" N4 C E 196 " 0.040 2.00e-02 2.50e+03 pdb=" C5 C E 196 " 0.017 2.00e-02 2.50e+03 pdb=" C6 C E 196 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 197 " 0.037 2.00e-02 2.50e+03 2.72e-02 1.66e+01 pdb=" N1 C E 197 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C E 197 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C E 197 " 0.015 2.00e-02 2.50e+03 pdb=" N3 C E 197 " -0.050 2.00e-02 2.50e+03 pdb=" C4 C E 197 " 0.018 2.00e-02 2.50e+03 pdb=" N4 C E 197 " 0.032 2.00e-02 2.50e+03 pdb=" C5 C E 197 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C E 197 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 4 " -0.021 2.00e-02 2.50e+03 1.78e-02 9.53e+00 pdb=" N9 DG C 4 " 0.038 2.00e-02 2.50e+03 pdb=" C8 DG C 4 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DG C 4 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DG C 4 " -0.021 2.00e-02 2.50e+03 pdb=" C6 DG C 4 " -0.011 2.00e-02 2.50e+03 pdb=" O6 DG C 4 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG C 4 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 4 " 0.011 2.00e-02 2.50e+03 pdb=" N2 DG C 4 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DG C 4 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DG C 4 " -0.009 2.00e-02 2.50e+03 ... (remaining 733 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1414 2.77 - 3.30: 5910 3.30 - 3.84: 14132 3.84 - 4.37: 16748 4.37 - 4.90: 23310 Nonbonded interactions: 61514 Sorted by model distance: nonbonded pdb=" O2' C E 152 " pdb=" OP1 G E 153 " model vdw 2.239 3.040 nonbonded pdb=" O SER A 52 " pdb=" OG SER A 52 " model vdw 2.244 3.040 nonbonded pdb=" O MET A 298 " pdb=" OG SER A 304 " model vdw 2.284 3.040 nonbonded pdb=" O2' A E 48 " pdb=" OP1 C E 49 " model vdw 2.284 3.040 nonbonded pdb=" OE1 GLU A 11 " pdb=" O2' G E 30 " model vdw 2.288 3.040 ... (remaining 61509 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=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.006 0.175 7962 Z= 0.351 Angle : 0.796 19.318 11674 Z= 0.452 Chirality : 0.047 0.349 1428 Planarity : 0.005 0.048 736 Dihedral : 26.191 177.894 4140 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.07 % Favored : 92.67 % Rotamer: Outliers : 4.37 % Allowed : 34.69 % Favored : 60.93 % 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: 0.24 (0.43), residues: 382 helix: 2.50 (0.40), residues: 167 sheet: -0.18 (0.89), residues: 41 loop : -2.29 (0.40), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 140 HIS 0.005 0.001 HIS A 99 PHE 0.014 0.002 PHE A 360 TYR 0.014 0.002 TYR A 44 ARG 0.004 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8216 (ttm) cc_final: 0.7928 (ttm) REVERT: A 188 ASN cc_start: 0.6485 (m-40) cc_final: 0.6041 (m110) REVERT: A 210 LYS cc_start: 0.8479 (mtpm) cc_final: 0.8094 (mmtm) REVERT: A 228 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 254 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7887 (mtm180) REVERT: A 301 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.8196 (tpp-160) REVERT: A 336 TRP cc_start: 0.8144 (m-90) cc_final: 0.7833 (m100) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 1.2388 time to fit residues: 82.7459 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 362 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7962 Z= 0.180 Angle : 0.635 10.488 11674 Z= 0.333 Chirality : 0.038 0.257 1428 Planarity : 0.004 0.042 736 Dihedral : 26.493 179.053 3352 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.02 % Favored : 93.72 % Rotamer: Outliers : 6.41 % Allowed : 29.45 % Favored : 64.14 % 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: 0.61 (0.44), residues: 382 helix: 2.83 (0.39), residues: 174 sheet: -0.05 (0.85), residues: 41 loop : -2.32 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 73 HIS 0.003 0.001 HIS A 99 PHE 0.010 0.001 PHE A 118 TYR 0.008 0.001 TYR A 33 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8168 (ttm) cc_final: 0.7907 (ttm) REVERT: A 127 ARG cc_start: 0.8311 (ptt180) cc_final: 0.7958 (ptt-90) REVERT: A 210 LYS cc_start: 0.8194 (mtpm) cc_final: 0.7773 (mmtm) REVERT: A 256 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8059 (mttp) REVERT: A 329 GLU cc_start: 0.8236 (pm20) cc_final: 0.7608 (pm20) REVERT: A 357 ASP cc_start: 0.7628 (p0) cc_final: 0.7077 (p0) outliers start: 22 outliers final: 8 residues processed: 61 average time/residue: 1.2107 time to fit residues: 78.3913 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 362 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 7962 Z= 0.538 Angle : 0.932 11.117 11674 Z= 0.485 Chirality : 0.054 0.372 1428 Planarity : 0.006 0.046 736 Dihedral : 26.943 178.338 3341 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.59 % Favored : 92.15 % Rotamer: Outliers : 7.00 % Allowed : 25.07 % Favored : 67.93 % 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: -0.32 (0.42), residues: 382 helix: 1.80 (0.39), residues: 174 sheet: -0.14 (0.83), residues: 41 loop : -2.59 (0.39), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 140 HIS 0.006 0.002 HIS A 39 PHE 0.029 0.003 PHE A 35 TYR 0.014 0.003 TYR A 171 ARG 0.009 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.556 Fit side-chains REVERT: A 106 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 210 LYS cc_start: 0.8377 (mtpm) cc_final: 0.7867 (mttm) outliers start: 24 outliers final: 12 residues processed: 58 average time/residue: 1.3316 time to fit residues: 81.4047 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 383 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7962 Z= 0.199 Angle : 0.652 10.761 11674 Z= 0.341 Chirality : 0.039 0.262 1428 Planarity : 0.004 0.040 736 Dihedral : 26.470 179.905 3339 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.54 % Favored : 93.19 % Rotamer: Outliers : 4.08 % Allowed : 28.28 % Favored : 67.64 % 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: 0.25 (0.43), residues: 382 helix: 2.49 (0.40), residues: 174 sheet: 0.34 (0.85), residues: 39 loop : -2.60 (0.39), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 336 HIS 0.003 0.001 HIS A 99 PHE 0.010 0.001 PHE A 118 TYR 0.011 0.001 TYR A 33 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8202 (ttm) cc_final: 0.7807 (ttm) REVERT: A 210 LYS cc_start: 0.8227 (mtpm) cc_final: 0.7748 (mttm) REVERT: A 254 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7824 (mtm180) REVERT: A 256 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8063 (mttp) REVERT: A 329 GLU cc_start: 0.8367 (pm20) cc_final: 0.7725 (pm20) REVERT: A 385 GLU cc_start: 0.7388 (pm20) cc_final: 0.7062 (pt0) outliers start: 14 outliers final: 7 residues processed: 49 average time/residue: 1.3276 time to fit residues: 68.7383 Evaluate side-chains 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7962 Z= 0.266 Angle : 0.701 10.215 11674 Z= 0.366 Chirality : 0.042 0.281 1428 Planarity : 0.004 0.042 736 Dihedral : 26.497 179.713 3339 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.54 % Favored : 93.19 % Rotamer: Outliers : 4.66 % Allowed : 27.70 % Favored : 67.64 % 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: 0.15 (0.43), residues: 382 helix: 2.41 (0.40), residues: 174 sheet: 0.13 (0.82), residues: 41 loop : -2.64 (0.39), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 140 HIS 0.004 0.001 HIS A 99 PHE 0.013 0.002 PHE A 35 TYR 0.012 0.002 TYR A 33 ARG 0.004 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.564 Fit side-chains REVERT: A 210 LYS cc_start: 0.8239 (mtpm) cc_final: 0.7743 (mttm) REVERT: A 254 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7862 (mtm180) REVERT: A 259 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9018 (mttt) REVERT: A 385 GLU cc_start: 0.7331 (pm20) cc_final: 0.7064 (pt0) outliers start: 16 outliers final: 8 residues processed: 50 average time/residue: 1.4686 time to fit residues: 77.2850 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7962 Z= 0.377 Angle : 0.797 10.498 11674 Z= 0.415 Chirality : 0.047 0.310 1428 Planarity : 0.005 0.044 736 Dihedral : 26.680 179.316 3339 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.33 % Favored : 92.41 % Rotamer: Outliers : 5.83 % Allowed : 26.53 % Favored : 67.64 % 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: -0.14 (0.43), residues: 382 helix: 2.05 (0.39), residues: 175 sheet: 0.01 (0.81), residues: 41 loop : -2.68 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 140 HIS 0.005 0.001 HIS A 99 PHE 0.018 0.002 PHE A 35 TYR 0.011 0.002 TYR A 33 ARG 0.006 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.544 Fit side-chains REVERT: A 210 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7788 (mttm) REVERT: A 385 GLU cc_start: 0.7314 (pm20) cc_final: 0.7045 (pt0) outliers start: 20 outliers final: 12 residues processed: 50 average time/residue: 1.3928 time to fit residues: 73.4598 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 383 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7962 Z= 0.161 Angle : 0.616 7.823 11674 Z= 0.322 Chirality : 0.037 0.252 1428 Planarity : 0.004 0.037 736 Dihedral : 26.321 178.356 3339 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.81 % Favored : 92.93 % Rotamer: Outliers : 4.08 % Allowed : 27.41 % Favored : 68.51 % 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: 0.51 (0.44), residues: 382 helix: 2.81 (0.40), residues: 171 sheet: 0.68 (0.85), residues: 39 loop : -2.55 (0.40), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 336 HIS 0.003 0.001 HIS A 99 PHE 0.009 0.001 PHE A 118 TYR 0.010 0.001 TYR A 33 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.470 Fit side-chains REVERT: A 210 LYS cc_start: 0.8197 (mtpm) cc_final: 0.7729 (mttm) REVERT: A 256 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8086 (mtmm) outliers start: 14 outliers final: 7 residues processed: 48 average time/residue: 1.3724 time to fit residues: 69.5538 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7962 Z= 0.396 Angle : 0.809 9.516 11674 Z= 0.421 Chirality : 0.047 0.310 1428 Planarity : 0.005 0.044 736 Dihedral : 26.606 177.902 3339 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.85 % Favored : 91.62 % Rotamer: Outliers : 3.50 % Allowed : 28.86 % Favored : 67.64 % 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: -0.10 (0.43), residues: 382 helix: 2.14 (0.39), residues: 174 sheet: 0.11 (0.80), residues: 41 loop : -2.72 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 140 HIS 0.005 0.001 HIS A 99 PHE 0.017 0.002 PHE A 35 TYR 0.010 0.002 TYR A 33 ARG 0.007 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8294 (mtpm) cc_final: 0.7786 (mttm) outliers start: 12 outliers final: 10 residues processed: 43 average time/residue: 1.2103 time to fit residues: 55.2840 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7962 Z= 0.333 Angle : 0.768 9.505 11674 Z= 0.401 Chirality : 0.045 0.296 1428 Planarity : 0.004 0.042 736 Dihedral : 26.579 177.448 3339 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.33 % Favored : 92.41 % Rotamer: Outliers : 4.37 % Allowed : 27.99 % Favored : 67.64 % 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: -0.14 (0.43), residues: 382 helix: 2.13 (0.39), residues: 174 sheet: -0.01 (0.81), residues: 41 loop : -2.73 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 336 HIS 0.004 0.001 HIS A 99 PHE 0.014 0.002 PHE A 35 TYR 0.012 0.002 TYR A 33 ARG 0.005 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8284 (mtpm) cc_final: 0.7777 (mttm) REVERT: A 254 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7791 (mtm180) REVERT: A 256 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8051 (mttp) outliers start: 15 outliers final: 10 residues processed: 45 average time/residue: 1.2616 time to fit residues: 60.0067 Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 ARG Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7962 Z= 0.320 Angle : 0.747 9.654 11674 Z= 0.390 Chirality : 0.044 0.293 1428 Planarity : 0.004 0.041 736 Dihedral : 26.538 177.042 3339 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 3.79 % Allowed : 28.86 % Favored : 67.35 % 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: -0.10 (0.43), residues: 382 helix: 2.12 (0.39), residues: 175 sheet: 0.14 (0.81), residues: 41 loop : -2.73 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 336 HIS 0.004 0.001 HIS A 99 PHE 0.013 0.002 PHE A 35 TYR 0.012 0.002 TYR A 33 ARG 0.005 0.001 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8275 (mtpm) cc_final: 0.7773 (mttm) outliers start: 13 outliers final: 10 residues processed: 46 average time/residue: 1.2372 time to fit residues: 60.3245 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.182469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.148700 restraints weight = 6886.050| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.68 r_work: 0.3134 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 200 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 204 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7962 Z= 0.318 Angle : 0.752 9.673 11674 Z= 0.393 Chirality : 0.044 0.293 1428 Planarity : 0.004 0.041 736 Dihedral : 26.541 177.155 3339 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.85 % Favored : 91.88 % Rotamer: Outliers : 4.66 % Allowed : 27.99 % Favored : 67.35 % 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: -0.12 (0.43), residues: 382 helix: 2.14 (0.40), residues: 174 sheet: 0.05 (0.81), residues: 41 loop : -2.74 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 336 HIS 0.004 0.001 HIS A 99 PHE 0.013 0.002 PHE A 35 TYR 0.013 0.002 TYR A 33 ARG 0.005 0.001 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.63 seconds wall clock time: 34 minutes 54.12 seconds (2094.12 seconds total)