Starting phenix.real_space_refine on Mon Sep 23 20:34:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/09_2024/7s8u_24922.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/09_2024/7s8u_24922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/09_2024/7s8u_24922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/09_2024/7s8u_24922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/09_2024/7s8u_24922.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s8u_24922/09_2024/7s8u_24922.cif" } resolution = 3.7 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= -0.004 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 3390 2.51 5 N 854 2.21 5 O 931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5210 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5210 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 30, 'TRANS': 636} Time building chain proxies: 3.54, per 1000 atoms: 0.68 Number of scatterers: 5210 At special positions: 0 Unit cell: (99.146, 100.26, 99.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 931 8.00 N 854 7.00 C 3390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 539 " - pdb=" SG CYS A 565 " distance=2.03 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: 1.30 Conformation dependent library (CDL) restraints added in 619.2 milliseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 55.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 15 through 45 Processing helix chain 'A' and resid 49 through 78 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 80 through 104 Processing helix chain 'A' and resid 120 through 153 Proline residue: A 142 - end of helix removed outlier: 5.023A pdb=" N SER A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 187 removed outlier: 3.535A pdb=" N SER A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 3.622A pdb=" N VAL A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 217 removed outlier: 4.033A pdb=" N ALA A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.643A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 249 removed outlier: 4.391A pdb=" N CYS A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 272 through 289 Processing helix chain 'A' and resid 291 through 311 removed outlier: 3.948A pdb=" N THR A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Proline residue: A 339 - end of helix removed outlier: 3.857A pdb=" N ASP A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 384 removed outlier: 3.556A pdb=" N ASP A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 609 Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 614 through 638 Processing helix chain 'A' and resid 644 through 669 removed outlier: 4.047A pdb=" N GLU A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 432 removed outlier: 8.225A pdb=" N HIS A 460 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN A 397 " --> pdb=" O HIS A 460 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE A 462 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS A 399 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL A 464 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 401 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA A 466 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A 465 " --> pdb=" O HIS A 469 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 419 Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 3.904A pdb=" N GLN A 519 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 488 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 486 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 554 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 574 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 555 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY A 572 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 557 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 570 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 510 removed outlier: 3.667A pdb=" N ASN A 509 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N PHE A 498 " --> pdb=" O ASN A 509 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 823 1.31 - 1.44: 1465 1.44 - 1.56: 2991 1.56 - 1.69: 0 1.69 - 1.82: 59 Bond restraints: 5338 Sorted by residual: bond pdb=" C TRP A 295 " pdb=" O TRP A 295 " ideal model delta sigma weight residual 1.237 1.301 -0.064 1.17e-02 7.31e+03 3.04e+01 bond pdb=" C LEU A 176 " pdb=" O LEU A 176 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.15e-02 7.56e+03 2.73e+01 bond pdb=" C VAL A 596 " pdb=" O VAL A 596 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.19e-02 7.06e+03 2.31e+01 bond pdb=" C GLY A 302 " pdb=" O GLY A 302 " ideal model delta sigma weight residual 1.235 1.297 -0.062 1.35e-02 5.49e+03 2.10e+01 bond pdb=" C PHE A 298 " pdb=" O PHE A 298 " ideal model delta sigma weight residual 1.236 1.288 -0.052 1.15e-02 7.56e+03 2.01e+01 ... (remaining 5333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 6769 2.41 - 4.82: 422 4.82 - 7.23: 52 7.23 - 9.64: 7 9.64 - 12.05: 1 Bond angle restraints: 7251 Sorted by residual: angle pdb=" CA PRO A 183 " pdb=" N PRO A 183 " pdb=" CD PRO A 183 " ideal model delta sigma weight residual 112.00 99.95 12.05 1.40e+00 5.10e-01 7.40e+01 angle pdb=" C PHE A 294 " pdb=" N TRP A 295 " pdb=" CA TRP A 295 " ideal model delta sigma weight residual 120.28 111.61 8.67 1.34e+00 5.57e-01 4.19e+01 angle pdb=" N GLN A 300 " pdb=" CA GLN A 300 " pdb=" C GLN A 300 " ideal model delta sigma weight residual 111.28 104.30 6.98 1.09e+00 8.42e-01 4.10e+01 angle pdb=" C LEU A 38 " pdb=" N ILE A 39 " pdb=" CA ILE A 39 " ideal model delta sigma weight residual 120.56 113.27 7.29 1.26e+00 6.30e-01 3.35e+01 angle pdb=" N GLN A 327 " pdb=" CA GLN A 327 " pdb=" C GLN A 327 " ideal model delta sigma weight residual 112.54 105.50 7.04 1.22e+00 6.72e-01 3.33e+01 ... (remaining 7246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 2834 16.07 - 32.14: 223 32.14 - 48.21: 57 48.21 - 64.28: 21 64.28 - 80.35: 8 Dihedral angle restraints: 3143 sinusoidal: 1218 harmonic: 1925 Sorted by residual: dihedral pdb=" C ILE A 585 " pdb=" N ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta harmonic sigma weight residual -122.00 -135.18 13.18 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta harmonic sigma weight residual 123.40 135.00 -11.60 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" C ILE A 289 " pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" CB ILE A 289 " ideal model delta harmonic sigma weight residual -122.00 -131.07 9.07 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 3140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 573 0.060 - 0.120: 180 0.120 - 0.181: 54 0.181 - 0.241: 18 0.241 - 0.301: 2 Chirality restraints: 827 Sorted by residual: chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE A 585 " pdb=" CA ILE A 585 " pdb=" CG1 ILE A 585 " pdb=" CG2 ILE A 585 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 824 not shown) Planarity restraints: 917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 182 " -0.082 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO A 183 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 302 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLY A 302 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY A 302 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 303 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 39 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ILE A 39 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 39 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 40 " 0.014 2.00e-02 2.50e+03 ... (remaining 914 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 983 2.77 - 3.31: 5547 3.31 - 3.84: 8613 3.84 - 4.37: 9757 4.37 - 4.90: 16386 Nonbonded interactions: 41286 Sorted by model distance: nonbonded pdb=" OG1 THR A 555 " pdb=" O PHE A 571 " model vdw 2.243 3.040 nonbonded pdb=" O VAL A 123 " pdb=" OG SER A 126 " model vdw 2.325 3.040 nonbonded pdb=" O GLN A 301 " pdb=" C GLY A 302 " model vdw 2.354 3.270 nonbonded pdb=" OG SER A 536 " pdb=" OE1 GLN A 538 " model vdw 2.367 3.040 nonbonded pdb=" O ILE A 56 " pdb=" OG1 THR A 59 " model vdw 2.382 3.040 ... (remaining 41281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 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 : 0.008 0.064 5338 Z= 0.505 Angle : 1.188 12.046 7251 Z= 0.848 Chirality : 0.070 0.301 827 Planarity : 0.007 0.117 917 Dihedral : 14.003 80.348 1904 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 1.20 % Allowed : 8.27 % Favored : 90.53 % Rotamer: Outliers : 4.56 % Allowed : 3.68 % Favored : 91.75 % Cbeta Deviations : 0.16 % 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: -1.14 (0.33), residues: 665 helix: 0.16 (0.28), residues: 339 sheet: 1.49 (0.72), residues: 54 loop : -2.48 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 622 HIS 0.004 0.001 HIS A 193 PHE 0.015 0.002 PHE A 356 TYR 0.025 0.002 TYR A 41 ARG 0.004 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 0.569 Fit side-chains REVERT: A 76 ASP cc_start: 0.6653 (t70) cc_final: 0.6325 (m-30) REVERT: A 183 PRO cc_start: 0.8466 (OUTLIER) cc_final: 0.7871 (Cg_endo) REVERT: A 286 PHE cc_start: 0.7024 (m-10) cc_final: 0.6651 (t80) REVERT: A 458 HIS cc_start: 0.4926 (m90) cc_final: 0.4489 (m90) REVERT: A 465 TRP cc_start: 0.3603 (p90) cc_final: 0.2983 (p90) REVERT: A 502 MET cc_start: 0.6655 (tmm) cc_final: 0.6420 (ppp) REVERT: A 541 ARG cc_start: 0.6430 (ptt180) cc_final: 0.6163 (ptt180) REVERT: A 632 ILE cc_start: 0.8696 (mt) cc_final: 0.8402 (mt) outliers start: 26 outliers final: 7 residues processed: 211 average time/residue: 0.1649 time to fit residues: 44.8009 Evaluate side-chains 156 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 183 PRO Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 PRO Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 586 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 193 HIS A 315 GLN A 519 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5338 Z= 0.238 Angle : 0.758 8.536 7251 Z= 0.403 Chirality : 0.049 0.217 827 Planarity : 0.006 0.068 917 Dihedral : 6.731 59.696 729 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.42 % Favored : 91.13 % Rotamer: Outliers : 4.39 % Allowed : 14.04 % Favored : 81.58 % 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: -0.72 (0.32), residues: 665 helix: 0.72 (0.27), residues: 353 sheet: 1.61 (0.66), residues: 52 loop : -2.72 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 622 HIS 0.007 0.002 HIS A 58 PHE 0.034 0.002 PHE A 243 TYR 0.021 0.002 TYR A 588 ARG 0.004 0.001 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.568 Fit side-chains REVERT: A 24 GLU cc_start: 0.7819 (tp30) cc_final: 0.7618 (tp30) REVERT: A 76 ASP cc_start: 0.6583 (t70) cc_final: 0.6261 (m-30) REVERT: A 285 MET cc_start: 0.7616 (ttp) cc_final: 0.7122 (mtp) REVERT: A 286 PHE cc_start: 0.6850 (m-10) cc_final: 0.6156 (t80) REVERT: A 301 GLN cc_start: 0.6077 (OUTLIER) cc_final: 0.4260 (tm130) REVERT: A 502 MET cc_start: 0.6050 (tmm) cc_final: 0.5850 (tmm) REVERT: A 541 ARG cc_start: 0.6348 (ptt180) cc_final: 0.6106 (ptt180) REVERT: A 595 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 632 ILE cc_start: 0.8814 (mt) cc_final: 0.8514 (mt) REVERT: A 644 LYS cc_start: 0.7331 (pttm) cc_final: 0.6872 (pttm) outliers start: 25 outliers final: 14 residues processed: 161 average time/residue: 0.1523 time to fit residues: 32.2500 Evaluate side-chains 147 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 585 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 49 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 277 GLN ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5338 Z= 0.212 Angle : 0.712 8.874 7251 Z= 0.372 Chirality : 0.046 0.210 827 Planarity : 0.005 0.071 917 Dihedral : 6.394 59.658 719 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.17 % Favored : 90.53 % Rotamer: Outliers : 4.21 % Allowed : 18.42 % Favored : 77.37 % 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: -0.44 (0.32), residues: 665 helix: 0.87 (0.27), residues: 354 sheet: 1.75 (0.68), residues: 52 loop : -2.50 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.027 0.002 PHE A 243 TYR 0.015 0.002 TYR A 224 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7629 (tp30) cc_final: 0.7412 (mm-30) REVERT: A 76 ASP cc_start: 0.6717 (t70) cc_final: 0.6365 (m-30) REVERT: A 126 SER cc_start: 0.8780 (p) cc_final: 0.8573 (p) REVERT: A 285 MET cc_start: 0.7419 (ttp) cc_final: 0.6972 (mtp) REVERT: A 286 PHE cc_start: 0.6779 (m-10) cc_final: 0.6105 (t80) REVERT: A 301 GLN cc_start: 0.6035 (OUTLIER) cc_final: 0.4371 (tm130) REVERT: A 371 MET cc_start: 0.7353 (mmm) cc_final: 0.6934 (mtp) REVERT: A 558 MET cc_start: 0.6212 (mmp) cc_final: 0.5866 (mmp) REVERT: A 595 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 632 ILE cc_start: 0.8784 (mt) cc_final: 0.8477 (mt) REVERT: A 644 LYS cc_start: 0.7337 (pttm) cc_final: 0.6963 (pttm) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.1341 time to fit residues: 26.9927 Evaluate side-chains 154 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5338 Z= 0.197 Angle : 0.681 8.517 7251 Z= 0.353 Chirality : 0.045 0.225 827 Planarity : 0.005 0.069 917 Dihedral : 5.973 54.996 717 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.57 % Favored : 91.13 % Rotamer: Outliers : 4.04 % Allowed : 20.88 % Favored : 75.09 % 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: -0.35 (0.32), residues: 665 helix: 0.96 (0.27), residues: 353 sheet: 1.88 (0.70), residues: 52 loop : -2.48 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.020 0.002 PHE A 243 TYR 0.018 0.001 TYR A 224 ARG 0.005 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 0.575 Fit side-chains REVERT: A 76 ASP cc_start: 0.6666 (t70) cc_final: 0.6364 (m-30) REVERT: A 126 SER cc_start: 0.8788 (p) cc_final: 0.8580 (p) REVERT: A 285 MET cc_start: 0.7392 (ttp) cc_final: 0.6953 (mtp) REVERT: A 286 PHE cc_start: 0.6804 (m-10) cc_final: 0.6136 (t80) REVERT: A 301 GLN cc_start: 0.5893 (OUTLIER) cc_final: 0.4355 (tm130) REVERT: A 327 GLN cc_start: 0.8780 (mp10) cc_final: 0.8575 (mp10) REVERT: A 541 ARG cc_start: 0.6225 (ptt180) cc_final: 0.5211 (mtm180) REVERT: A 558 MET cc_start: 0.6264 (mmp) cc_final: 0.6054 (mmp) REVERT: A 595 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7726 (tm-30) REVERT: A 632 ILE cc_start: 0.8786 (mt) cc_final: 0.8495 (mt) REVERT: A 644 LYS cc_start: 0.7370 (pttm) cc_final: 0.7019 (pttm) outliers start: 23 outliers final: 18 residues processed: 151 average time/residue: 0.1432 time to fit residues: 28.7638 Evaluate side-chains 148 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 277 GLN A 458 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5338 Z= 0.201 Angle : 0.706 10.035 7251 Z= 0.362 Chirality : 0.044 0.172 827 Planarity : 0.005 0.064 917 Dihedral : 5.942 55.413 717 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.02 % Favored : 90.68 % Rotamer: Outliers : 4.91 % Allowed : 21.93 % Favored : 73.16 % 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 (0.33), residues: 665 helix: 1.08 (0.27), residues: 354 sheet: 1.70 (0.70), residues: 52 loop : -2.43 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 622 HIS 0.009 0.002 HIS A 193 PHE 0.028 0.002 PHE A 356 TYR 0.018 0.001 TYR A 224 ARG 0.002 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 0.561 Fit side-chains REVERT: A 76 ASP cc_start: 0.6592 (t70) cc_final: 0.6288 (m-30) REVERT: A 126 SER cc_start: 0.8781 (p) cc_final: 0.8543 (p) REVERT: A 285 MET cc_start: 0.7382 (ttp) cc_final: 0.6980 (mtp) REVERT: A 286 PHE cc_start: 0.6900 (m-10) cc_final: 0.6234 (t80) REVERT: A 301 GLN cc_start: 0.6069 (OUTLIER) cc_final: 0.4517 (tm130) REVERT: A 371 MET cc_start: 0.7170 (mmm) cc_final: 0.6901 (mtt) REVERT: A 541 ARG cc_start: 0.6154 (ptt180) cc_final: 0.5937 (mtm180) REVERT: A 595 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 632 ILE cc_start: 0.8793 (mt) cc_final: 0.8511 (mt) REVERT: A 644 LYS cc_start: 0.7416 (pttm) cc_final: 0.7055 (pttm) outliers start: 28 outliers final: 25 residues processed: 146 average time/residue: 0.1353 time to fit residues: 26.8412 Evaluate side-chains 151 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 507 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 458 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5338 Z= 0.205 Angle : 0.697 8.282 7251 Z= 0.360 Chirality : 0.044 0.165 827 Planarity : 0.005 0.058 917 Dihedral : 5.928 55.843 717 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.87 % Favored : 90.83 % Rotamer: Outliers : 5.79 % Allowed : 22.28 % Favored : 71.93 % 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: -0.29 (0.33), residues: 665 helix: 1.08 (0.27), residues: 354 sheet: 1.71 (0.69), residues: 52 loop : -2.55 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 622 HIS 0.006 0.001 HIS A 58 PHE 0.018 0.001 PHE A 356 TYR 0.019 0.002 TYR A 224 ARG 0.002 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 0.571 Fit side-chains REVERT: A 76 ASP cc_start: 0.6528 (t70) cc_final: 0.6274 (m-30) REVERT: A 126 SER cc_start: 0.8796 (p) cc_final: 0.8547 (p) REVERT: A 285 MET cc_start: 0.7412 (ttp) cc_final: 0.6998 (mtp) REVERT: A 286 PHE cc_start: 0.6970 (m-10) cc_final: 0.6255 (t80) REVERT: A 301 GLN cc_start: 0.6056 (OUTLIER) cc_final: 0.4538 (tm130) REVERT: A 327 GLN cc_start: 0.8862 (mp10) cc_final: 0.8655 (mp10) REVERT: A 357 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.5581 (p) REVERT: A 371 MET cc_start: 0.7354 (mmm) cc_final: 0.7008 (mtt) REVERT: A 541 ARG cc_start: 0.6304 (ptt180) cc_final: 0.5657 (mtm180) REVERT: A 558 MET cc_start: 0.5854 (mmp) cc_final: 0.5422 (mmp) REVERT: A 632 ILE cc_start: 0.8796 (mt) cc_final: 0.8508 (mt) REVERT: A 644 LYS cc_start: 0.7450 (pttm) cc_final: 0.7083 (pttm) outliers start: 33 outliers final: 27 residues processed: 147 average time/residue: 0.1630 time to fit residues: 32.9436 Evaluate side-chains 157 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 458 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5338 Z= 0.188 Angle : 0.685 8.166 7251 Z= 0.349 Chirality : 0.044 0.168 827 Planarity : 0.005 0.056 917 Dihedral : 5.823 58.024 717 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.72 % Favored : 90.98 % Rotamer: Outliers : 5.61 % Allowed : 22.81 % Favored : 71.58 % 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: -0.19 (0.33), residues: 665 helix: 1.17 (0.27), residues: 354 sheet: 1.66 (0.67), residues: 52 loop : -2.47 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 622 HIS 0.005 0.001 HIS A 58 PHE 0.025 0.001 PHE A 356 TYR 0.014 0.001 TYR A 41 ARG 0.002 0.000 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 76 ASP cc_start: 0.6528 (t70) cc_final: 0.6282 (m-30) REVERT: A 126 SER cc_start: 0.8802 (p) cc_final: 0.8547 (p) REVERT: A 225 LYS cc_start: 0.7528 (tppt) cc_final: 0.7313 (tttt) REVERT: A 285 MET cc_start: 0.7390 (ttp) cc_final: 0.6968 (mtp) REVERT: A 286 PHE cc_start: 0.6878 (m-10) cc_final: 0.6329 (t80) REVERT: A 301 GLN cc_start: 0.5711 (OUTLIER) cc_final: 0.4324 (tm130) REVERT: A 311 THR cc_start: 0.7939 (p) cc_final: 0.7631 (t) REVERT: A 357 THR cc_start: 0.5850 (OUTLIER) cc_final: 0.5358 (p) REVERT: A 371 MET cc_start: 0.7444 (mmm) cc_final: 0.7067 (mtt) REVERT: A 417 MET cc_start: 0.4100 (mmm) cc_final: 0.3776 (ptm) REVERT: A 556 TYR cc_start: 0.6769 (m-10) cc_final: 0.6476 (m-10) REVERT: A 558 MET cc_start: 0.5683 (mmp) cc_final: 0.5263 (mmp) REVERT: A 632 ILE cc_start: 0.8745 (mt) cc_final: 0.8444 (mt) REVERT: A 644 LYS cc_start: 0.7456 (pttm) cc_final: 0.7138 (pttm) outliers start: 32 outliers final: 28 residues processed: 146 average time/residue: 0.1893 time to fit residues: 38.9762 Evaluate side-chains 154 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 458 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5338 Z= 0.227 Angle : 0.720 8.353 7251 Z= 0.370 Chirality : 0.045 0.197 827 Planarity : 0.005 0.054 917 Dihedral : 5.939 57.761 717 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.62 % Favored : 90.23 % Rotamer: Outliers : 7.02 % Allowed : 21.93 % Favored : 71.05 % 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: -0.23 (0.33), residues: 665 helix: 1.13 (0.28), residues: 354 sheet: 1.23 (0.68), residues: 54 loop : -2.40 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 646 HIS 0.020 0.002 HIS A 193 PHE 0.020 0.002 PHE A 356 TYR 0.016 0.002 TYR A 41 ARG 0.005 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 76 ASP cc_start: 0.6565 (t70) cc_final: 0.6308 (m-30) REVERT: A 126 SER cc_start: 0.8812 (p) cc_final: 0.8611 (p) REVERT: A 285 MET cc_start: 0.7499 (ttp) cc_final: 0.7104 (mtp) REVERT: A 286 PHE cc_start: 0.6910 (m-10) cc_final: 0.6325 (t80) REVERT: A 301 GLN cc_start: 0.5645 (OUTLIER) cc_final: 0.4155 (tm130) REVERT: A 311 THR cc_start: 0.8042 (p) cc_final: 0.7735 (t) REVERT: A 357 THR cc_start: 0.6292 (OUTLIER) cc_final: 0.5828 (p) REVERT: A 556 TYR cc_start: 0.6962 (m-10) cc_final: 0.6653 (m-10) REVERT: A 558 MET cc_start: 0.6038 (mmp) cc_final: 0.5580 (mmp) REVERT: A 632 ILE cc_start: 0.8858 (mt) cc_final: 0.8567 (mt) REVERT: A 644 LYS cc_start: 0.7521 (pttm) cc_final: 0.7151 (pttm) REVERT: A 657 LEU cc_start: 0.7235 (tp) cc_final: 0.6990 (mt) outliers start: 40 outliers final: 30 residues processed: 151 average time/residue: 0.1546 time to fit residues: 31.5697 Evaluate side-chains 157 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS A 458 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5338 Z= 0.245 Angle : 0.781 9.797 7251 Z= 0.397 Chirality : 0.046 0.173 827 Planarity : 0.005 0.051 917 Dihedral : 6.433 77.620 717 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.32 % Favored : 90.53 % Rotamer: Outliers : 6.14 % Allowed : 23.86 % Favored : 70.00 % 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: -0.46 (0.32), residues: 665 helix: 1.03 (0.27), residues: 353 sheet: 1.10 (0.68), residues: 54 loop : -2.65 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 646 HIS 0.009 0.002 HIS A 251 PHE 0.032 0.002 PHE A 356 TYR 0.016 0.002 TYR A 41 ARG 0.006 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 0.534 Fit side-chains REVERT: A 18 PHE cc_start: 0.3694 (OUTLIER) cc_final: 0.3438 (m-80) REVERT: A 76 ASP cc_start: 0.6617 (t70) cc_final: 0.6294 (m-30) REVERT: A 126 SER cc_start: 0.8882 (p) cc_final: 0.8639 (p) REVERT: A 285 MET cc_start: 0.7535 (ttp) cc_final: 0.7146 (mtp) REVERT: A 286 PHE cc_start: 0.6916 (m-10) cc_final: 0.6097 (t80) REVERT: A 301 GLN cc_start: 0.5858 (OUTLIER) cc_final: 0.4022 (tm130) REVERT: A 357 THR cc_start: 0.6580 (OUTLIER) cc_final: 0.6131 (p) REVERT: A 417 MET cc_start: 0.4107 (mmm) cc_final: 0.3823 (ptm) REVERT: A 558 MET cc_start: 0.6153 (mmp) cc_final: 0.5672 (mmp) REVERT: A 632 ILE cc_start: 0.8872 (mt) cc_final: 0.8596 (mt) REVERT: A 644 LYS cc_start: 0.7380 (pttm) cc_final: 0.7004 (pttm) REVERT: A 657 LEU cc_start: 0.7369 (tp) cc_final: 0.7119 (mt) outliers start: 35 outliers final: 28 residues processed: 150 average time/residue: 0.1336 time to fit residues: 27.3708 Evaluate side-chains 160 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 14 optimal weight: 9.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5338 Z= 0.207 Angle : 0.744 11.689 7251 Z= 0.376 Chirality : 0.046 0.192 827 Planarity : 0.005 0.048 917 Dihedral : 6.059 61.436 717 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.87 % Favored : 90.98 % Rotamer: Outliers : 4.91 % Allowed : 25.26 % Favored : 69.82 % 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: -0.40 (0.33), residues: 665 helix: 1.01 (0.27), residues: 353 sheet: 0.92 (0.69), residues: 56 loop : -2.47 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 622 HIS 0.026 0.003 HIS A 193 PHE 0.016 0.001 PHE A 373 TYR 0.016 0.002 TYR A 41 ARG 0.002 0.000 ARG A 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.563 Fit side-chains REVERT: A 76 ASP cc_start: 0.6600 (t70) cc_final: 0.6283 (m-30) REVERT: A 126 SER cc_start: 0.8868 (p) cc_final: 0.8629 (p) REVERT: A 285 MET cc_start: 0.7526 (ttp) cc_final: 0.7155 (mtp) REVERT: A 286 PHE cc_start: 0.6702 (m-10) cc_final: 0.6058 (t80) REVERT: A 301 GLN cc_start: 0.5764 (OUTLIER) cc_final: 0.4222 (tm130) REVERT: A 357 THR cc_start: 0.6355 (OUTLIER) cc_final: 0.6049 (p) REVERT: A 417 MET cc_start: 0.4043 (mmm) cc_final: 0.3772 (ptm) REVERT: A 558 MET cc_start: 0.5996 (mmp) cc_final: 0.5596 (mmp) REVERT: A 632 ILE cc_start: 0.8789 (mt) cc_final: 0.8482 (mt) REVERT: A 644 LYS cc_start: 0.7341 (pttm) cc_final: 0.6404 (pttm) REVERT: A 648 GLU cc_start: 0.7056 (mp0) cc_final: 0.6728 (pm20) REVERT: A 657 LEU cc_start: 0.7391 (tp) cc_final: 0.7102 (mt) outliers start: 28 outliers final: 23 residues processed: 147 average time/residue: 0.1333 time to fit residues: 26.8283 Evaluate side-chains 154 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 666 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.221774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.200119 restraints weight = 11227.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.205153 restraints weight = 6880.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.205634 restraints weight = 4051.899| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5338 Z= 0.212 Angle : 0.753 10.971 7251 Z= 0.380 Chirality : 0.046 0.185 827 Planarity : 0.005 0.049 917 Dihedral : 6.048 57.703 717 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.17 % Favored : 90.68 % Rotamer: Outliers : 4.39 % Allowed : 26.14 % Favored : 69.47 % 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: -0.39 (0.33), residues: 665 helix: 0.98 (0.27), residues: 353 sheet: 0.76 (0.68), residues: 56 loop : -2.37 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 295 HIS 0.006 0.001 HIS A 251 PHE 0.030 0.001 PHE A 356 TYR 0.015 0.002 TYR A 41 ARG 0.003 0.000 ARG A 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.52 seconds wall clock time: 28 minutes 29.38 seconds (1709.38 seconds total)