Starting phenix.real_space_refine on Thu Nov 14 10:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/11_2024/8k0b_36759.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/11_2024/8k0b_36759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/11_2024/8k0b_36759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/11_2024/8k0b_36759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/11_2024/8k0b_36759.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/11_2024/8k0b_36759.cif" } resolution = 3.56 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= 0.020 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 34 5.16 5 C 3758 2.51 5 N 945 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5689 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5689 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 25, 'TRANS': 663} Time building chain proxies: 3.62, per 1000 atoms: 0.64 Number of scatterers: 5689 At special positions: 0 Unit cell: (104.94, 93.28, 92.22, 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 34 16.00 O 952 8.00 N 945 7.00 C 3758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 300 " 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: 1.45 Conformation dependent library (CDL) restraints added in 627.3 milliseconds 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 64.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 35 through 61 Processing helix chain 'A' and resid 63 through 73 removed outlier: 4.353A pdb=" N ALA A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.619A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 removed outlier: 3.959A pdb=" N ALA A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 146 removed outlier: 3.653A pdb=" N ARG A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 140 " --> pdb=" O HIS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 182 through 206 Processing helix chain 'A' and resid 231 through 243 removed outlier: 4.030A pdb=" N ILE A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 285 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.944A pdb=" N ARG A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 334 removed outlier: 4.135A pdb=" N GLN A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.725A pdb=" N VAL A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 406 through 429 Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 446 through 477 removed outlier: 4.132A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Proline residue: A 454 - end of helix Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 480 through 502 removed outlier: 3.968A pdb=" N TYR A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 540 through 560 removed outlier: 4.238A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 574 removed outlier: 3.833A pdb=" N CYS A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.777A pdb=" N VAL A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 617 through 640 removed outlier: 3.938A pdb=" N PHE A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 661 removed outlier: 3.950A pdb=" N HIS A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 656 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 677 removed outlier: 3.856A pdb=" N GLY A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.696A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 255 removed outlier: 5.716A pdb=" N LEU A 340 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 223 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A 382 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 318 hydrogen bonds defined for protein. 939 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: 1.66 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 832 1.31 - 1.44: 1783 1.44 - 1.56: 3192 1.56 - 1.69: 0 1.69 - 1.82: 51 Bond restraints: 5858 Sorted by residual: bond pdb=" C TYR A 130 " pdb=" O TYR A 130 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.32e+01 bond pdb=" CA TYR A 130 " pdb=" C TYR A 130 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" CA SER A 687 " pdb=" CB SER A 687 " ideal model delta sigma weight residual 1.530 1.478 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" N TYR A 54 " pdb=" CA TYR A 54 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.82e+00 bond pdb=" N SER A 689 " pdb=" CA SER A 689 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.10e+00 ... (remaining 5853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 7860 3.25 - 6.51: 82 6.51 - 9.76: 14 9.76 - 13.01: 3 13.01 - 16.27: 2 Bond angle restraints: 7961 Sorted by residual: angle pdb=" C TYR A 130 " pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " ideal model delta sigma weight residual 110.96 94.69 16.27 1.54e+00 4.22e-01 1.12e+02 angle pdb=" N HIS A 136 " pdb=" CA HIS A 136 " pdb=" C HIS A 136 " ideal model delta sigma weight residual 112.87 102.31 10.56 1.20e+00 6.94e-01 7.74e+01 angle pdb=" N SER A 687 " pdb=" CA SER A 687 " pdb=" C SER A 687 " ideal model delta sigma weight residual 111.11 101.72 9.39 1.20e+00 6.94e-01 6.12e+01 angle pdb=" C ILE A 131 " pdb=" N THR A 132 " pdb=" CA THR A 132 " ideal model delta sigma weight residual 120.79 111.26 9.53 1.39e+00 5.18e-01 4.70e+01 angle pdb=" C HIS A 136 " pdb=" CA HIS A 136 " pdb=" CB HIS A 136 " ideal model delta sigma weight residual 110.21 124.85 -14.64 2.19e+00 2.09e-01 4.47e+01 ... (remaining 7956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2883 17.46 - 34.91: 389 34.91 - 52.37: 104 52.37 - 69.83: 22 69.83 - 87.29: 9 Dihedral angle restraints: 3407 sinusoidal: 1361 harmonic: 2046 Sorted by residual: dihedral pdb=" C TYR A 130 " pdb=" N TYR A 130 " pdb=" CA TYR A 130 " pdb=" CB TYR A 130 " ideal model delta harmonic sigma weight residual -122.60 -103.89 -18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" CA LEU A 536 " pdb=" C LEU A 536 " pdb=" N PRO A 537 " pdb=" CA PRO A 537 " ideal model delta harmonic sigma weight residual 180.00 147.47 32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 300 " pdb=" CB CYS A 300 " ideal model delta sinusoidal sigma weight residual 93.00 145.30 -52.30 1 1.00e+01 1.00e-02 3.73e+01 ... (remaining 3404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 737 0.057 - 0.114: 139 0.114 - 0.171: 11 0.171 - 0.228: 7 0.228 - 0.286: 2 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA TYR A 130 " pdb=" N TYR A 130 " pdb=" C TYR A 130 " pdb=" CB TYR A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA HIS A 136 " pdb=" N HIS A 136 " pdb=" C HIS A 136 " pdb=" CB HIS A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA GLN A 134 " pdb=" N GLN A 134 " pdb=" C GLN A 134 " pdb=" CB GLN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 893 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 128 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ARG A 128 " -0.068 2.00e-02 2.50e+03 pdb=" O ARG A 128 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE A 129 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 671 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C PHE A 671 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE A 671 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 672 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 193 " -0.031 2.00e-02 2.50e+03 2.11e-02 8.87e+00 pdb=" CG TYR A 193 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 193 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 193 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 193 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 193 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 193 " -0.005 2.00e-02 2.50e+03 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 439 2.74 - 3.28: 5992 3.28 - 3.82: 9520 3.82 - 4.36: 10716 4.36 - 4.90: 17742 Nonbonded interactions: 44409 Sorted by model distance: nonbonded pdb=" OD1 ASN A 636 " pdb=" OG SER A 640 " model vdw 2.195 3.040 nonbonded pdb=" O ASP A 520 " pdb=" NH1 ARG A 530 " model vdw 2.281 3.120 nonbonded pdb=" O PHE A 420 " pdb=" OG1 THR A 424 " model vdw 2.282 3.040 nonbonded pdb=" OD1 ASP A 339 " pdb=" NH2 ARG A 400 " model vdw 2.325 3.120 nonbonded pdb=" OG1 THR A 278 " pdb=" OE2 GLU A 312 " model vdw 2.338 3.040 ... (remaining 44404 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.300 Find NCS groups from input model: 0.040 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5858 Z= 0.239 Angle : 0.865 16.268 7961 Z= 0.506 Chirality : 0.047 0.286 896 Planarity : 0.005 0.057 974 Dihedral : 17.336 87.286 2080 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.28 % Allowed : 31.31 % Favored : 67.41 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.63 (0.33), residues: 687 helix: 0.59 (0.27), residues: 398 sheet: 0.92 (1.28), residues: 17 loop : -2.07 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 479 HIS 0.003 0.001 HIS A 362 PHE 0.022 0.001 PHE A 519 TYR 0.049 0.002 TYR A 193 ARG 0.003 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 131 ILE cc_start: 0.6800 (tt) cc_final: 0.6532 (tp) REVERT: A 221 MET cc_start: 0.4513 (tmm) cc_final: 0.3930 (ppp) REVERT: A 671 PHE cc_start: 0.7396 (t80) cc_final: 0.7137 (t80) REVERT: A 688 MET cc_start: 0.6435 (tpp) cc_final: 0.6142 (tpp) outliers start: 8 outliers final: 2 residues processed: 108 average time/residue: 0.1671 time to fit residues: 24.1692 Evaluate side-chains 106 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 691 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.0060 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 197 ASN A 593 GLN A 630 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5858 Z= 0.194 Angle : 0.662 12.636 7961 Z= 0.342 Chirality : 0.043 0.170 896 Planarity : 0.004 0.059 974 Dihedral : 5.418 55.136 766 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.71 % Allowed : 26.36 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.43 (0.33), residues: 687 helix: 0.77 (0.27), residues: 404 sheet: 0.98 (1.33), residues: 17 loop : -2.07 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 668 HIS 0.005 0.001 HIS A 362 PHE 0.023 0.001 PHE A 140 TYR 0.040 0.002 TYR A 193 ARG 0.003 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.4627 (tmm) cc_final: 0.4312 (ppp) REVERT: A 411 ILE cc_start: 0.7302 (tp) cc_final: 0.7048 (mt) REVERT: A 437 VAL cc_start: -0.2155 (OUTLIER) cc_final: -0.2943 (m) REVERT: A 522 TYR cc_start: 0.1229 (OUTLIER) cc_final: -0.0486 (m-80) REVERT: A 646 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.3852 (pp) REVERT: A 688 MET cc_start: 0.5387 (tpp) cc_final: 0.5140 (tpp) REVERT: A 690 SER cc_start: 0.7823 (t) cc_final: 0.7264 (p) outliers start: 42 outliers final: 23 residues processed: 141 average time/residue: 0.1558 time to fit residues: 29.5749 Evaluate side-chains 129 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 593 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 703 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5858 Z= 0.209 Angle : 0.682 15.553 7961 Z= 0.349 Chirality : 0.043 0.167 896 Planarity : 0.004 0.061 974 Dihedral : 5.176 46.881 766 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.03 % Allowed : 25.24 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: 687 helix: 0.80 (0.27), residues: 407 sheet: 0.89 (1.30), residues: 17 loop : -2.10 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 479 HIS 0.005 0.001 HIS A 362 PHE 0.026 0.001 PHE A 168 TYR 0.039 0.002 TYR A 193 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 VAL cc_start: 0.6886 (p) cc_final: 0.6051 (m) REVERT: A 411 ILE cc_start: 0.7293 (tp) cc_final: 0.7070 (mt) REVERT: A 433 ASP cc_start: 0.4423 (OUTLIER) cc_final: 0.3353 (p0) REVERT: A 437 VAL cc_start: -0.2212 (OUTLIER) cc_final: -0.3036 (m) REVERT: A 479 TRP cc_start: 0.6325 (m100) cc_final: 0.5413 (m100) REVERT: A 500 VAL cc_start: 0.7089 (p) cc_final: 0.6865 (p) REVERT: A 534 VAL cc_start: 0.5300 (OUTLIER) cc_final: 0.5050 (m) REVERT: A 565 LEU cc_start: 0.2490 (OUTLIER) cc_final: 0.2269 (mm) REVERT: A 598 TYR cc_start: 0.7476 (m-80) cc_final: 0.7143 (m-80) REVERT: A 604 VAL cc_start: 0.8235 (t) cc_final: 0.8019 (t) REVERT: A 608 VAL cc_start: 0.7699 (t) cc_final: 0.7490 (p) REVERT: A 646 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.4134 (pp) outliers start: 44 outliers final: 29 residues processed: 143 average time/residue: 0.1523 time to fit residues: 29.5889 Evaluate side-chains 138 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 136 HIS A 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5359 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5858 Z= 0.185 Angle : 0.669 14.942 7961 Z= 0.338 Chirality : 0.043 0.167 896 Planarity : 0.004 0.060 974 Dihedral : 4.892 32.927 764 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 7.03 % Allowed : 26.36 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.34 (0.33), residues: 687 helix: 0.86 (0.27), residues: 407 sheet: 0.57 (1.20), residues: 17 loop : -2.08 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 479 HIS 0.004 0.001 HIS A 362 PHE 0.026 0.001 PHE A 140 TYR 0.036 0.002 TYR A 193 ARG 0.009 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5594 (t80) cc_final: 0.5391 (t80) REVERT: A 209 VAL cc_start: 0.6862 (p) cc_final: 0.6020 (m) REVERT: A 406 THR cc_start: 0.7332 (p) cc_final: 0.7130 (t) REVERT: A 411 ILE cc_start: 0.7288 (tp) cc_final: 0.7069 (mt) REVERT: A 433 ASP cc_start: 0.4403 (OUTLIER) cc_final: 0.3372 (p0) REVERT: A 437 VAL cc_start: -0.2251 (OUTLIER) cc_final: -0.3049 (m) REVERT: A 499 MET cc_start: 0.5962 (mmp) cc_final: 0.5728 (mmp) REVERT: A 534 VAL cc_start: 0.5269 (OUTLIER) cc_final: 0.5001 (m) REVERT: A 565 LEU cc_start: 0.2436 (OUTLIER) cc_final: 0.2113 (mm) REVERT: A 598 TYR cc_start: 0.7456 (m-80) cc_final: 0.6775 (m-80) REVERT: A 646 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.3938 (pp) REVERT: A 685 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6170 (mm) outliers start: 44 outliers final: 31 residues processed: 137 average time/residue: 0.1587 time to fit residues: 29.4207 Evaluate side-chains 136 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 40.0000 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 59 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5858 Z= 0.230 Angle : 0.699 14.158 7961 Z= 0.356 Chirality : 0.043 0.168 896 Planarity : 0.005 0.061 974 Dihedral : 4.839 32.464 764 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 8.31 % Allowed : 25.56 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.43 (0.33), residues: 687 helix: 0.70 (0.27), residues: 412 sheet: 0.55 (1.21), residues: 17 loop : -1.99 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 479 HIS 0.006 0.001 HIS A 362 PHE 0.029 0.001 PHE A 140 TYR 0.040 0.002 TYR A 193 ARG 0.006 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5624 (t80) cc_final: 0.5346 (t80) REVERT: A 271 MET cc_start: 0.3257 (OUTLIER) cc_final: 0.3054 (tpt) REVERT: A 411 ILE cc_start: 0.7297 (tp) cc_final: 0.7085 (mt) REVERT: A 433 ASP cc_start: 0.4396 (OUTLIER) cc_final: 0.3133 (p0) REVERT: A 437 VAL cc_start: -0.2156 (OUTLIER) cc_final: -0.3038 (m) REVERT: A 534 VAL cc_start: 0.5225 (OUTLIER) cc_final: 0.4907 (m) REVERT: A 565 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.2178 (mm) REVERT: A 598 TYR cc_start: 0.7467 (m-80) cc_final: 0.6006 (m-80) REVERT: A 646 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.4507 (pp) REVERT: A 685 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6251 (mm) outliers start: 52 outliers final: 33 residues processed: 143 average time/residue: 0.1531 time to fit residues: 29.7036 Evaluate side-chains 141 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5399 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5858 Z= 0.208 Angle : 0.705 14.978 7961 Z= 0.355 Chirality : 0.044 0.180 896 Planarity : 0.004 0.061 974 Dihedral : 4.672 32.980 762 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 7.99 % Allowed : 26.68 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.43 (0.33), residues: 687 helix: 0.71 (0.26), residues: 412 sheet: 0.52 (1.18), residues: 17 loop : -2.01 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 479 HIS 0.005 0.001 HIS A 136 PHE 0.024 0.001 PHE A 140 TYR 0.038 0.002 TYR A 193 ARG 0.005 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5633 (t80) cc_final: 0.5339 (t80) REVERT: A 411 ILE cc_start: 0.7371 (tp) cc_final: 0.7144 (mt) REVERT: A 433 ASP cc_start: 0.4057 (OUTLIER) cc_final: 0.2943 (p0) REVERT: A 437 VAL cc_start: -0.2154 (OUTLIER) cc_final: -0.3025 (m) REVERT: A 522 TYR cc_start: 0.1118 (OUTLIER) cc_final: -0.0601 (m-80) REVERT: A 534 VAL cc_start: 0.5206 (OUTLIER) cc_final: 0.4960 (m) REVERT: A 565 LEU cc_start: 0.1831 (OUTLIER) cc_final: 0.1596 (mm) REVERT: A 598 TYR cc_start: 0.7357 (m-80) cc_final: 0.5822 (m-80) REVERT: A 646 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.4524 (pp) REVERT: A 685 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6166 (mm) REVERT: A 690 SER cc_start: 0.7807 (t) cc_final: 0.7190 (p) outliers start: 50 outliers final: 32 residues processed: 143 average time/residue: 0.1692 time to fit residues: 32.3926 Evaluate side-chains 138 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.0570 chunk 37 optimal weight: 0.0370 chunk 55 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.0040 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5858 Z= 0.165 Angle : 0.687 14.151 7961 Z= 0.344 Chirality : 0.042 0.167 896 Planarity : 0.004 0.060 974 Dihedral : 4.546 33.062 762 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.87 % Allowed : 27.64 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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 (0.34), residues: 687 helix: 0.83 (0.27), residues: 412 sheet: 0.74 (1.22), residues: 17 loop : -1.98 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 668 HIS 0.004 0.001 HIS A 136 PHE 0.028 0.001 PHE A 140 TYR 0.023 0.001 TYR A 625 ARG 0.005 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5556 (t80) cc_final: 0.5268 (t80) REVERT: A 411 ILE cc_start: 0.7286 (tp) cc_final: 0.7075 (mt) REVERT: A 437 VAL cc_start: -0.2176 (OUTLIER) cc_final: -0.2959 (m) REVERT: A 512 HIS cc_start: 0.7153 (OUTLIER) cc_final: 0.6662 (p-80) REVERT: A 522 TYR cc_start: 0.1409 (OUTLIER) cc_final: -0.0340 (m-80) REVERT: A 534 VAL cc_start: 0.5216 (OUTLIER) cc_final: 0.4946 (m) REVERT: A 598 TYR cc_start: 0.7318 (m-80) cc_final: 0.5761 (m-80) REVERT: A 646 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.4278 (pp) REVERT: A 685 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6144 (mm) REVERT: A 690 SER cc_start: 0.7794 (t) cc_final: 0.7115 (p) outliers start: 43 outliers final: 27 residues processed: 132 average time/residue: 0.1619 time to fit residues: 28.9331 Evaluate side-chains 133 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5858 Z= 0.203 Angle : 0.719 14.981 7961 Z= 0.361 Chirality : 0.043 0.155 896 Planarity : 0.005 0.060 974 Dihedral : 4.600 32.795 762 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 6.07 % Allowed : 29.07 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: 687 helix: 0.81 (0.27), residues: 406 sheet: 0.51 (1.16), residues: 17 loop : -2.06 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 479 HIS 0.004 0.001 HIS A 366 PHE 0.027 0.001 PHE A 140 TYR 0.021 0.002 TYR A 193 ARG 0.004 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5638 (t80) cc_final: 0.5356 (t80) REVERT: A 411 ILE cc_start: 0.7375 (tp) cc_final: 0.7149 (mt) REVERT: A 427 ILE cc_start: 0.7984 (mm) cc_final: 0.7620 (mp) REVERT: A 433 ASP cc_start: 0.4018 (OUTLIER) cc_final: 0.3005 (p0) REVERT: A 437 VAL cc_start: -0.2143 (OUTLIER) cc_final: -0.2978 (m) REVERT: A 522 TYR cc_start: 0.1201 (OUTLIER) cc_final: -0.0632 (m-80) REVERT: A 534 VAL cc_start: 0.5337 (OUTLIER) cc_final: 0.5064 (m) REVERT: A 598 TYR cc_start: 0.7335 (m-80) cc_final: 0.5780 (m-80) REVERT: A 671 PHE cc_start: 0.7560 (t80) cc_final: 0.7203 (t80) REVERT: A 685 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.6155 (mm) REVERT: A 690 SER cc_start: 0.7807 (t) cc_final: 0.7130 (p) outliers start: 38 outliers final: 29 residues processed: 129 average time/residue: 0.1601 time to fit residues: 27.8907 Evaluate side-chains 131 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 20.0000 chunk 57 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5858 Z= 0.195 Angle : 0.733 15.020 7961 Z= 0.364 Chirality : 0.044 0.191 896 Planarity : 0.004 0.061 974 Dihedral : 4.585 32.758 762 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.07 % Allowed : 29.23 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.37 (0.34), residues: 687 helix: 0.79 (0.27), residues: 407 sheet: 0.74 (1.18), residues: 17 loop : -2.01 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 479 HIS 0.006 0.001 HIS A 651 PHE 0.025 0.001 PHE A 140 TYR 0.020 0.002 TYR A 193 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.7885 (t) cc_final: 0.7512 (p) REVERT: A 411 ILE cc_start: 0.7361 (tp) cc_final: 0.7142 (mt) REVERT: A 427 ILE cc_start: 0.8049 (mm) cc_final: 0.7608 (mp) REVERT: A 433 ASP cc_start: 0.3969 (OUTLIER) cc_final: 0.3014 (p0) REVERT: A 437 VAL cc_start: -0.2167 (OUTLIER) cc_final: -0.2997 (m) REVERT: A 522 TYR cc_start: 0.1214 (OUTLIER) cc_final: -0.0597 (m-80) REVERT: A 534 VAL cc_start: 0.5327 (OUTLIER) cc_final: 0.5071 (m) REVERT: A 598 TYR cc_start: 0.7299 (m-80) cc_final: 0.5788 (m-80) REVERT: A 685 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.6132 (mm) REVERT: A 690 SER cc_start: 0.7775 (t) cc_final: 0.7116 (p) outliers start: 38 outliers final: 30 residues processed: 130 average time/residue: 0.1556 time to fit residues: 27.1636 Evaluate side-chains 133 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 136 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5858 Z= 0.201 Angle : 0.745 15.014 7961 Z= 0.369 Chirality : 0.044 0.155 896 Planarity : 0.005 0.060 974 Dihedral : 4.590 32.553 762 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.59 % Allowed : 30.35 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.38 (0.33), residues: 687 helix: 0.80 (0.27), residues: 405 sheet: 0.83 (1.18), residues: 17 loop : -2.03 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 479 HIS 0.005 0.001 HIS A 651 PHE 0.025 0.001 PHE A 140 TYR 0.020 0.002 TYR A 193 ARG 0.004 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.7878 (t) cc_final: 0.7552 (p) REVERT: A 411 ILE cc_start: 0.7364 (tp) cc_final: 0.7140 (mt) REVERT: A 427 ILE cc_start: 0.8050 (mm) cc_final: 0.7612 (mp) REVERT: A 433 ASP cc_start: 0.3916 (OUTLIER) cc_final: 0.2923 (p0) REVERT: A 437 VAL cc_start: -0.2179 (OUTLIER) cc_final: -0.3030 (m) REVERT: A 522 TYR cc_start: 0.1133 (OUTLIER) cc_final: -0.0709 (m-80) REVERT: A 534 VAL cc_start: 0.5380 (OUTLIER) cc_final: 0.5098 (m) REVERT: A 598 TYR cc_start: 0.7281 (m-80) cc_final: 0.5817 (m-80) REVERT: A 671 PHE cc_start: 0.7634 (t80) cc_final: 0.7310 (t80) REVERT: A 685 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6144 (mm) REVERT: A 690 SER cc_start: 0.7774 (t) cc_final: 0.7114 (p) outliers start: 35 outliers final: 27 residues processed: 129 average time/residue: 0.1673 time to fit residues: 30.4423 Evaluate side-chains 132 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 404 TRP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 526 HIS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.0020 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.0000 overall best weight: 0.2470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 197 ASN ** 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 = 0.4905 r_free = 0.4905 target = 0.241070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.207290 restraints weight = 10662.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.211288 restraints weight = 5501.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.213878 restraints weight = 3559.809| |-----------------------------------------------------------------------------| r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5858 Z= 0.179 Angle : 0.740 14.936 7961 Z= 0.364 Chirality : 0.043 0.217 896 Planarity : 0.004 0.060 974 Dihedral : 4.545 32.989 762 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.75 % Allowed : 30.67 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -0.34 (0.34), residues: 687 helix: 0.85 (0.27), residues: 405 sheet: 0.85 (1.18), residues: 17 loop : -2.05 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 668 HIS 0.005 0.001 HIS A 651 PHE 0.025 0.001 PHE A 140 TYR 0.025 0.002 TYR A 625 ARG 0.003 0.000 ARG A 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1504.63 seconds wall clock time: 28 minutes 6.46 seconds (1686.46 seconds total)