Starting phenix.real_space_refine on Fri Dec 27 13:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehw_28153/12_2024/8ehw_28153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehw_28153/12_2024/8ehw_28153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ehw_28153/12_2024/8ehw_28153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehw_28153/12_2024/8ehw_28153.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehw_28153/12_2024/8ehw_28153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehw_28153/12_2024/8ehw_28153.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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 32 5.16 5 C 3410 2.51 5 N 826 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5150 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5150 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 25, 'TRANS': 604} Chain breaks: 2 Time building chain proxies: 3.68, per 1000 atoms: 0.71 Number of scatterers: 5150 At special positions: 0 Unit cell: (97.35, 107.25, 75.9, 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 32 16.00 O 882 8.00 N 826 7.00 C 3410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 315 " distance=2.80 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: 1.25 Conformation dependent library (CDL) restraints added in 523.7 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 70.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 45 through 48 removed outlier: 3.722A pdb=" N GLY A 48 " --> pdb=" O VAL A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 49 through 75 removed outlier: 3.593A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.750A pdb=" N ILE A 120 " --> pdb=" O TRP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 167 removed outlier: 3.966A pdb=" N HIS A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 191 through 219 removed outlier: 4.165A pdb=" N LEU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 Processing helix chain 'A' and resid 266 through 294 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 320 through 342 removed outlier: 3.546A pdb=" N ARG A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.822A pdb=" N ALA A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.585A pdb=" N LEU A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 415 through 445 removed outlier: 3.522A pdb=" N TRP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 466 through 491 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 499 through 515 removed outlier: 3.645A pdb=" N PHE A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 534 removed outlier: 3.682A pdb=" N SER A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 553 through 565 removed outlier: 4.298A pdb=" N VAL A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 574 through 587 removed outlier: 3.526A pdb=" N MET A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 606 through 624 removed outlier: 3.740A pdb=" N TYR A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 650 removed outlier: 4.038A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 672 removed outlier: 4.045A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 690 removed outlier: 3.743A pdb=" N ILE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.943A pdb=" N LEU A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 264 removed outlier: 5.626A pdb=" N VAL A 257 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR A 353 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP A 259 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 351 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLN A 261 " --> pdb=" O MET A 349 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET A 349 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 263 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299 306 hydrogen bonds defined for protein. 873 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: 1.44 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1339 1.34 - 1.46: 1155 1.46 - 1.58: 2751 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 5292 Sorted by residual: bond pdb=" N VAL A 451 " pdb=" CA VAL A 451 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N VAL A 342 " pdb=" CA VAL A 342 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.38e+00 bond pdb=" N LYS A 453 " pdb=" CA LYS A 453 " ideal model delta sigma weight residual 1.460 1.481 -0.021 7.10e-03 1.98e+04 8.35e+00 bond pdb=" N CYS A 32 " pdb=" CA CYS A 32 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.25e-02 6.40e+03 7.64e+00 bond pdb=" N VAL A 266 " pdb=" CA VAL A 266 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.08e+00 ... (remaining 5287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 7001 2.72 - 5.44: 165 5.44 - 8.16: 18 8.16 - 10.88: 3 10.88 - 13.60: 4 Bond angle restraints: 7191 Sorted by residual: angle pdb=" C VAL A 342 " pdb=" CA VAL A 342 " pdb=" CB VAL A 342 " ideal model delta sigma weight residual 111.29 100.02 11.27 1.64e+00 3.72e-01 4.73e+01 angle pdb=" C LEU A 641 " pdb=" CA LEU A 641 " pdb=" CB LEU A 641 " ideal model delta sigma weight residual 110.81 121.73 -10.92 1.60e+00 3.91e-01 4.66e+01 angle pdb=" N VAL A 342 " pdb=" CA VAL A 342 " pdb=" C VAL A 342 " ideal model delta sigma weight residual 109.34 122.94 -13.60 2.08e+00 2.31e-01 4.28e+01 angle pdb=" N LEU A 641 " pdb=" CA LEU A 641 " pdb=" C LEU A 641 " ideal model delta sigma weight residual 111.11 105.62 5.49 1.20e+00 6.94e-01 2.09e+01 angle pdb=" N GLU A 338 " pdb=" CA GLU A 338 " pdb=" C GLU A 338 " ideal model delta sigma weight residual 111.33 116.13 -4.80 1.21e+00 6.83e-01 1.57e+01 ... (remaining 7186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2651 17.84 - 35.67: 343 35.67 - 53.51: 95 53.51 - 71.34: 9 71.34 - 89.18: 2 Dihedral angle restraints: 3100 sinusoidal: 1236 harmonic: 1864 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 315 " pdb=" CB CYS A 315 " ideal model delta sinusoidal sigma weight residual -86.00 -18.06 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" C LEU A 641 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " pdb=" CB LEU A 641 " ideal model delta harmonic sigma weight residual -122.60 -133.39 10.79 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" CA PRO A 550 " pdb=" C PRO A 550 " pdb=" N ASP A 551 " pdb=" CA ASP A 551 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 660 0.060 - 0.120: 137 0.120 - 0.180: 21 0.180 - 0.240: 5 0.240 - 0.300: 2 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA LEU A 641 " pdb=" N LEU A 641 " pdb=" C LEU A 641 " pdb=" CB LEU A 641 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA TYR A 624 " pdb=" N TYR A 624 " pdb=" C TYR A 624 " pdb=" CB TYR A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE A 270 " pdb=" N ILE A 270 " pdb=" C ILE A 270 " pdb=" CB ILE A 270 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 822 not shown) Planarity restraints: 877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 338 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" CD GLU A 338 " 0.070 2.00e-02 2.50e+03 pdb=" OE1 GLU A 338 " -0.025 2.00e-02 2.50e+03 pdb=" OE2 GLU A 338 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 341 " -0.034 2.00e-02 2.50e+03 2.57e-02 9.89e+00 pdb=" CG HIS A 341 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 341 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS A 341 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS A 341 " -0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS A 341 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 549 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.16e+00 pdb=" N PRO A 550 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " 0.042 5.00e-02 4.00e+02 ... (remaining 874 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1295 2.79 - 3.32: 5400 3.32 - 3.84: 8746 3.84 - 4.37: 9798 4.37 - 4.90: 16052 Nonbonded interactions: 41291 Sorted by model distance: nonbonded pdb=" N PHE A 47 " pdb=" O TYR A 176 " model vdw 2.262 3.120 nonbonded pdb=" NZ LYS A 448 " pdb=" OD1 ASP A 551 " model vdw 2.354 3.120 nonbonded pdb=" O ARG A 595 " pdb=" NE2 GLN A 599 " model vdw 2.359 3.120 nonbonded pdb=" NH1 ARG A 530 " pdb=" OD2 ASP A 534 " model vdw 2.387 3.120 nonbonded pdb=" O TRP A 194 " pdb=" OG1 THR A 197 " model vdw 2.412 3.040 ... (remaining 41286 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: 1.070 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: 15.640 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 0.043 5292 Z= 0.358 Angle : 0.970 13.601 7191 Z= 0.564 Chirality : 0.053 0.300 825 Planarity : 0.007 0.076 877 Dihedral : 16.572 89.180 1884 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.18 % Allowed : 31.23 % Favored : 68.60 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.34), residues: 624 helix: -0.27 (0.26), residues: 386 sheet: 1.22 (1.35), residues: 16 loop : -1.29 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 422 HIS 0.010 0.001 HIS A 341 PHE 0.035 0.002 PHE A 307 TYR 0.037 0.003 TYR A 323 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.8775 (m-80) cc_final: 0.7875 (m-80) REVERT: A 323 TYR cc_start: 0.8960 (t80) cc_final: 0.8142 (t80) REVERT: A 332 LEU cc_start: 0.9428 (tp) cc_final: 0.9214 (mt) REVERT: A 365 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8732 (mmtt) REVERT: A 502 MET cc_start: 0.7755 (tpt) cc_final: 0.7178 (tpt) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1949 time to fit residues: 28.5139 Evaluate side-chains 96 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 450 ASN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5292 Z= 0.264 Angle : 0.697 10.059 7191 Z= 0.350 Chirality : 0.045 0.225 825 Planarity : 0.005 0.050 877 Dihedral : 4.592 20.216 681 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.68 % Allowed : 27.89 % Favored : 68.42 % 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 (0.35), residues: 624 helix: 0.95 (0.27), residues: 391 sheet: 0.34 (1.11), residues: 22 loop : -0.95 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 681 HIS 0.005 0.001 HIS A 341 PHE 0.016 0.001 PHE A 199 TYR 0.023 0.002 TYR A 286 ARG 0.004 0.001 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.9027 (m-80) cc_final: 0.8639 (m-80) REVERT: A 327 MET cc_start: 0.9191 (mtp) cc_final: 0.8864 (mtp) REVERT: A 333 GLU cc_start: 0.8780 (tt0) cc_final: 0.8105 (tp30) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 0.1869 time to fit residues: 30.7842 Evaluate side-chains 101 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5292 Z= 0.250 Angle : 0.701 12.505 7191 Z= 0.340 Chirality : 0.044 0.138 825 Planarity : 0.004 0.035 877 Dihedral : 4.512 19.257 681 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.96 % Allowed : 26.84 % Favored : 67.19 % 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: 0.54 (0.35), residues: 624 helix: 1.05 (0.27), residues: 390 sheet: 0.45 (1.10), residues: 22 loop : -0.87 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 681 HIS 0.004 0.001 HIS A 341 PHE 0.010 0.001 PHE A 430 TYR 0.018 0.002 TYR A 286 ARG 0.003 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7383 (t0) cc_final: 0.6565 (t0) REVERT: A 286 TYR cc_start: 0.9012 (m-80) cc_final: 0.8736 (m-10) REVERT: A 324 TYR cc_start: 0.8950 (m-80) cc_final: 0.8637 (m-80) REVERT: A 327 MET cc_start: 0.9185 (mtp) cc_final: 0.8980 (mtm) REVERT: A 333 GLU cc_start: 0.8924 (tt0) cc_final: 0.8146 (tp30) REVERT: A 570 MET cc_start: 0.8709 (tpt) cc_final: 0.8272 (tpt) REVERT: A 606 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7621 (pm20) outliers start: 34 outliers final: 12 residues processed: 129 average time/residue: 0.1456 time to fit residues: 25.6034 Evaluate side-chains 109 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5292 Z= 0.175 Angle : 0.675 11.513 7191 Z= 0.321 Chirality : 0.042 0.129 825 Planarity : 0.004 0.037 877 Dihedral : 4.403 18.740 681 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.79 % Allowed : 26.32 % Favored : 67.89 % 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 (0.35), residues: 624 helix: 1.12 (0.27), residues: 390 sheet: 0.49 (1.05), residues: 22 loop : -0.64 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 681 HIS 0.007 0.001 HIS A 648 PHE 0.011 0.001 PHE A 583 TYR 0.015 0.001 TYR A 323 ARG 0.003 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7346 (t0) cc_final: 0.6551 (t0) REVERT: A 286 TYR cc_start: 0.8995 (m-80) cc_final: 0.8646 (m-10) REVERT: A 327 MET cc_start: 0.9224 (mtp) cc_final: 0.8957 (mtp) REVERT: A 333 GLU cc_start: 0.8960 (tt0) cc_final: 0.8082 (tp30) REVERT: A 443 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7385 (mp) REVERT: A 570 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8294 (tpt) REVERT: A 606 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7532 (pm20) outliers start: 33 outliers final: 16 residues processed: 123 average time/residue: 0.1464 time to fit residues: 25.4163 Evaluate side-chains 114 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN A 290 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5292 Z= 0.218 Angle : 0.695 13.100 7191 Z= 0.329 Chirality : 0.043 0.155 825 Planarity : 0.004 0.036 877 Dihedral : 4.392 18.495 681 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.79 % Allowed : 26.67 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.35), residues: 624 helix: 0.96 (0.26), residues: 393 sheet: 0.36 (1.01), residues: 22 loop : -0.55 (0.48), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 681 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.001 PHE A 583 TYR 0.029 0.002 TYR A 286 ARG 0.004 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7377 (t0) cc_final: 0.6632 (t0) REVERT: A 323 TYR cc_start: 0.9005 (t80) cc_final: 0.8750 (t80) REVERT: A 327 MET cc_start: 0.9235 (mtp) cc_final: 0.8837 (mtp) REVERT: A 333 GLU cc_start: 0.8981 (tt0) cc_final: 0.8130 (tp30) REVERT: A 422 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.7276 (t60) REVERT: A 443 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 502 MET cc_start: 0.7721 (tpt) cc_final: 0.7230 (tpt) REVERT: A 606 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7727 (pm20) outliers start: 33 outliers final: 20 residues processed: 127 average time/residue: 0.1464 time to fit residues: 25.2391 Evaluate side-chains 120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 422 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 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 185 ASN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5292 Z= 0.177 Angle : 0.692 13.678 7191 Z= 0.325 Chirality : 0.042 0.141 825 Planarity : 0.003 0.037 877 Dihedral : 4.324 18.233 681 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.04 % Allowed : 30.00 % Favored : 65.96 % 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: 0.58 (0.35), residues: 624 helix: 0.91 (0.26), residues: 397 sheet: 0.33 (0.99), residues: 22 loop : -0.52 (0.49), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 681 HIS 0.003 0.000 HIS A 341 PHE 0.024 0.001 PHE A 680 TYR 0.019 0.002 TYR A 286 ARG 0.004 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7457 (t0) cc_final: 0.6691 (t0) REVERT: A 327 MET cc_start: 0.9242 (mtp) cc_final: 0.8994 (mtp) REVERT: A 333 GLU cc_start: 0.8988 (tt0) cc_final: 0.8164 (tp30) REVERT: A 502 MET cc_start: 0.7766 (tpt) cc_final: 0.7372 (tpt) REVERT: A 606 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7654 (pm20) outliers start: 23 outliers final: 20 residues processed: 116 average time/residue: 0.1610 time to fit residues: 24.6888 Evaluate side-chains 119 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5292 Z= 0.193 Angle : 0.702 13.789 7191 Z= 0.328 Chirality : 0.042 0.143 825 Planarity : 0.003 0.037 877 Dihedral : 4.258 17.922 681 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.39 % Allowed : 28.95 % Favored : 66.67 % 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 (0.35), residues: 624 helix: 0.92 (0.26), residues: 397 sheet: 0.34 (1.00), residues: 22 loop : -0.45 (0.50), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.023 0.001 PHE A 680 TYR 0.025 0.002 TYR A 323 ARG 0.003 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7059 (m-30) cc_final: 0.6570 (t0) REVERT: A 185 ASN cc_start: 0.7427 (t0) cc_final: 0.6718 (t0) REVERT: A 327 MET cc_start: 0.9255 (mtp) cc_final: 0.8966 (mtp) REVERT: A 333 GLU cc_start: 0.9007 (tt0) cc_final: 0.8194 (tp30) REVERT: A 502 MET cc_start: 0.7769 (tpt) cc_final: 0.7295 (tpt) REVERT: A 570 MET cc_start: 0.8603 (tpt) cc_final: 0.8303 (tpt) REVERT: A 606 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7631 (pm20) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.1491 time to fit residues: 23.8073 Evaluate side-chains 118 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5292 Z= 0.198 Angle : 0.705 14.456 7191 Z= 0.330 Chirality : 0.042 0.144 825 Planarity : 0.003 0.036 877 Dihedral : 4.291 17.957 681 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.21 % Allowed : 29.30 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.35), residues: 624 helix: 1.05 (0.26), residues: 391 sheet: 0.23 (1.00), residues: 22 loop : -0.31 (0.50), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.012 0.001 PHE A 583 TYR 0.028 0.002 TYR A 324 ARG 0.003 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7022 (m-30) cc_final: 0.6509 (t0) REVERT: A 185 ASN cc_start: 0.7373 (t0) cc_final: 0.6679 (t0) REVERT: A 331 LEU cc_start: 0.9408 (mt) cc_final: 0.9203 (pp) REVERT: A 333 GLU cc_start: 0.8992 (tt0) cc_final: 0.8193 (tp30) REVERT: A 502 MET cc_start: 0.7782 (tpt) cc_final: 0.7298 (tpt) REVERT: A 606 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7619 (pm20) outliers start: 24 outliers final: 22 residues processed: 118 average time/residue: 0.1529 time to fit residues: 24.7661 Evaluate side-chains 120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.0170 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5292 Z= 0.180 Angle : 0.704 14.559 7191 Z= 0.332 Chirality : 0.042 0.145 825 Planarity : 0.003 0.035 877 Dihedral : 4.283 17.790 681 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.39 % Allowed : 29.65 % Favored : 65.96 % 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: 0.80 (0.35), residues: 624 helix: 1.05 (0.26), residues: 391 sheet: 0.27 (1.00), residues: 22 loop : -0.29 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.026 0.001 PHE A 680 TYR 0.021 0.002 TYR A 324 ARG 0.003 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.6961 (m-30) cc_final: 0.6434 (t0) REVERT: A 185 ASN cc_start: 0.7336 (t0) cc_final: 0.6683 (t0) REVERT: A 323 TYR cc_start: 0.9211 (t80) cc_final: 0.8978 (t80) REVERT: A 324 TYR cc_start: 0.8580 (m-10) cc_final: 0.8288 (m-10) REVERT: A 333 GLU cc_start: 0.9010 (tt0) cc_final: 0.8217 (tp30) REVERT: A 502 MET cc_start: 0.7748 (tpt) cc_final: 0.7309 (tpt) REVERT: A 571 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8212 (tm-30) REVERT: A 601 GLN cc_start: 0.6829 (tp40) cc_final: 0.6055 (tm-30) REVERT: A 606 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7515 (pm20) outliers start: 25 outliers final: 24 residues processed: 119 average time/residue: 0.2058 time to fit residues: 34.4723 Evaluate side-chains 122 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 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 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5292 Z= 0.174 Angle : 0.730 17.863 7191 Z= 0.337 Chirality : 0.042 0.162 825 Planarity : 0.003 0.035 877 Dihedral : 4.280 17.406 681 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.39 % Allowed : 29.12 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.35), residues: 624 helix: 0.97 (0.26), residues: 391 sheet: 0.21 (0.99), residues: 22 loop : -0.23 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.018 0.001 PHE A 63 TYR 0.019 0.002 TYR A 324 ARG 0.003 0.000 ARG A 689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.6930 (m-30) cc_final: 0.6426 (t0) REVERT: A 185 ASN cc_start: 0.7342 (t0) cc_final: 0.6756 (t0) REVERT: A 323 TYR cc_start: 0.9224 (t80) cc_final: 0.8988 (t80) REVERT: A 328 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9083 (pptt) REVERT: A 329 ASP cc_start: 0.9314 (m-30) cc_final: 0.8363 (m-30) REVERT: A 333 GLU cc_start: 0.9000 (tt0) cc_final: 0.8223 (tp30) REVERT: A 349 MET cc_start: 0.6935 (mmp) cc_final: 0.6615 (mmp) REVERT: A 460 ASN cc_start: 0.7787 (t0) cc_final: 0.7504 (t0) REVERT: A 502 MET cc_start: 0.7730 (tpt) cc_final: 0.7300 (tpt) REVERT: A 601 GLN cc_start: 0.6846 (tp40) cc_final: 0.6015 (tm-30) REVERT: A 606 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7806 (mt-10) outliers start: 25 outliers final: 22 residues processed: 120 average time/residue: 0.1526 time to fit residues: 24.7060 Evaluate side-chains 118 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.170140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.116752 restraints weight = 8668.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120186 restraints weight = 5232.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.122385 restraints weight = 3995.137| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5292 Z= 0.283 Angle : 0.781 16.141 7191 Z= 0.369 Chirality : 0.045 0.194 825 Planarity : 0.004 0.032 877 Dihedral : 4.362 18.319 681 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.56 % Allowed : 30.00 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.35), residues: 624 helix: 0.68 (0.26), residues: 399 sheet: 0.78 (1.20), residues: 17 loop : -0.37 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 681 HIS 0.003 0.001 HIS A 214 PHE 0.016 0.001 PHE A 63 TYR 0.030 0.002 TYR A 324 ARG 0.002 0.000 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1478.58 seconds wall clock time: 28 minutes 54.65 seconds (1734.65 seconds total)