Starting phenix.real_space_refine on Sun Mar 10 22:35:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/03_2024/8k0b_36759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/03_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_36759/03_2024/8k0b_36759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/03_2024/8k0b_36759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/03_2024/8k0b_36759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0b_36759/03_2024/8k0b_36759.pdb" } 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 Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.94, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 988.6 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: 0.52 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: 1.61 Time building geometry restraints manager: 2.56 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: 94.69 - 102.57: 23 102.57 - 110.44: 1379 110.44 - 118.31: 3073 118.31 - 126.19: 3371 126.19 - 134.06: 115 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 2.440 nonbonded pdb=" O ASP A 520 " pdb=" NH1 ARG A 530 " model vdw 2.281 2.520 nonbonded pdb=" O PHE A 420 " pdb=" OG1 THR A 424 " model vdw 2.282 2.440 nonbonded pdb=" OD1 ASP A 339 " pdb=" NH2 ARG A 400 " model vdw 2.325 2.520 nonbonded pdb=" OG1 THR A 278 " pdb=" OE2 GLU A 312 " model vdw 2.338 2.440 ... (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: 1.530 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: 3.690 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.250 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.581 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: 0.1803 time to fit residues: 26.0400 Evaluate side-chains 106 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.5380 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5858 Z= 0.224 Angle : 0.667 13.411 7961 Z= 0.345 Chirality : 0.043 0.172 896 Planarity : 0.004 0.059 974 Dihedral : 5.480 54.373 766 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 7.19 % Allowed : 26.36 % Favored : 66.45 % 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: 0.79 (0.27), residues: 402 sheet: 0.82 (1.29), residues: 17 loop : -2.09 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 668 HIS 0.007 0.001 HIS A 362 PHE 0.024 0.001 PHE A 168 TYR 0.044 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 154 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 109 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.5632 (m-70) cc_final: 0.5427 (m-70) REVERT: A 168 PHE cc_start: 0.8106 (t80) cc_final: 0.7579 (t80) REVERT: A 209 VAL cc_start: 0.6880 (p) cc_final: 0.6044 (m) REVERT: A 221 MET cc_start: 0.4712 (tmm) cc_final: 0.4278 (ppp) REVERT: A 411 ILE cc_start: 0.7297 (tp) cc_final: 0.7075 (mt) REVERT: A 437 VAL cc_start: -0.2332 (OUTLIER) cc_final: -0.3182 (m) REVERT: A 479 TRP cc_start: 0.6430 (m100) cc_final: 0.5334 (m100) REVERT: A 522 TYR cc_start: 0.1243 (OUTLIER) cc_final: -0.0484 (m-80) REVERT: A 598 TYR cc_start: 0.7275 (m-80) cc_final: 0.6901 (m-80) REVERT: A 646 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.4110 (pp) REVERT: A 671 PHE cc_start: 0.7306 (t80) cc_final: 0.6677 (t80) outliers start: 45 outliers final: 30 residues processed: 142 average time/residue: 0.1540 time to fit residues: 29.3403 Evaluate side-chains 134 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 163 ASP 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 406 THR 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 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 560 MET 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 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 691 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 42 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.0070 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** 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: 0.5305 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5858 Z= 0.154 Angle : 0.630 15.540 7961 Z= 0.317 Chirality : 0.041 0.177 896 Planarity : 0.004 0.060 974 Dihedral : 5.020 43.228 766 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.87 % Allowed : 26.52 % 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: -0.21 (0.34), residues: 687 helix: 1.00 (0.27), residues: 404 sheet: 0.97 (1.30), residues: 17 loop : -2.08 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 479 HIS 0.002 0.000 HIS A 651 PHE 0.026 0.001 PHE A 140 TYR 0.033 0.001 TYR A 193 ARG 0.002 0.000 ARG A 170 *********************** 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 145 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6368 (tp40) cc_final: 0.6026 (mm-40) REVERT: A 209 VAL cc_start: 0.6888 (p) cc_final: 0.6070 (m) REVERT: A 411 ILE cc_start: 0.7294 (tp) cc_final: 0.7063 (mt) REVERT: A 437 VAL cc_start: -0.1949 (OUTLIER) cc_final: -0.2730 (m) REVERT: A 500 VAL cc_start: 0.6984 (p) cc_final: 0.6754 (t) REVERT: A 522 TYR cc_start: 0.1226 (OUTLIER) cc_final: -0.0494 (m-80) REVERT: A 534 VAL cc_start: 0.5086 (OUTLIER) cc_final: 0.4853 (m) REVERT: A 598 TYR cc_start: 0.7244 (m-80) cc_final: 0.5968 (m-80) REVERT: A 646 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.3943 (pp) REVERT: A 664 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6135 (mt) outliers start: 43 outliers final: 26 residues processed: 138 average time/residue: 0.1539 time to fit residues: 28.5442 Evaluate side-chains 132 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 163 ASP 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 496 LEU 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 529 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 560 MET 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 664 LEU 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 713 TYR 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: 0.5980 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 0.0000 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.0270 chunk 0 optimal weight: 0.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS A 197 ASN ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5858 Z= 0.172 Angle : 0.636 14.251 7961 Z= 0.321 Chirality : 0.042 0.171 896 Planarity : 0.004 0.059 974 Dihedral : 4.790 33.231 764 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 7.19 % Allowed : 28.12 % 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: -0.17 (0.34), residues: 687 helix: 1.06 (0.27), residues: 402 sheet: 0.61 (1.22), residues: 17 loop : -2.04 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 668 HIS 0.003 0.001 HIS A 362 PHE 0.026 0.001 PHE A 140 TYR 0.033 0.001 TYR A 193 ARG 0.002 0.000 ARG A 170 *********************** 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 148 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6404 (tp40) cc_final: 0.6061 (mm-40) REVERT: A 209 VAL cc_start: 0.6882 (p) cc_final: 0.6030 (m) REVERT: A 411 ILE cc_start: 0.7296 (tp) cc_final: 0.7075 (mt) REVERT: A 433 ASP cc_start: 0.4447 (OUTLIER) cc_final: 0.3215 (p0) REVERT: A 437 VAL cc_start: -0.2175 (OUTLIER) cc_final: -0.2971 (m) REVERT: A 500 VAL cc_start: 0.6997 (p) cc_final: 0.6745 (t) REVERT: A 522 TYR cc_start: 0.1238 (OUTLIER) cc_final: -0.0665 (m-80) REVERT: A 536 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6307 (mp) REVERT: A 565 LEU cc_start: 0.1807 (OUTLIER) cc_final: 0.1593 (mm) REVERT: A 598 TYR cc_start: 0.7233 (m-80) cc_final: 0.5894 (m-80) REVERT: A 646 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.4079 (pp) REVERT: A 664 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6168 (mt) outliers start: 45 outliers final: 28 residues processed: 137 average time/residue: 0.1542 time to fit residues: 28.5124 Evaluate side-chains 137 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 ASP 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 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 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 536 LEU Chi-restraints excluded: chain A residue 560 MET 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 664 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 59 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN A 657 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5858 Z= 0.209 Angle : 0.664 14.746 7961 Z= 0.335 Chirality : 0.042 0.175 896 Planarity : 0.004 0.060 974 Dihedral : 4.820 33.347 764 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 7.83 % Allowed : 27.64 % Favored : 64.54 % 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: -0.21 (0.34), residues: 687 helix: 0.96 (0.27), residues: 407 sheet: 0.70 (1.24), residues: 17 loop : -2.01 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 668 HIS 0.005 0.001 HIS A 362 PHE 0.030 0.001 PHE A 140 TYR 0.036 0.002 TYR A 193 ARG 0.003 0.000 ARG A 268 *********************** 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 154 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 105 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6460 (tp40) cc_final: 0.6156 (mm-40) REVERT: A 168 PHE cc_start: 0.7944 (t80) cc_final: 0.7679 (t80) REVERT: A 411 ILE cc_start: 0.7302 (tp) cc_final: 0.7083 (mt) REVERT: A 433 ASP cc_start: 0.4436 (OUTLIER) cc_final: 0.3077 (p0) REVERT: A 437 VAL cc_start: -0.2313 (OUTLIER) cc_final: -0.3173 (m) REVERT: A 457 LEU cc_start: 0.7835 (tp) cc_final: 0.7418 (tp) REVERT: A 500 VAL cc_start: 0.7106 (p) cc_final: 0.6836 (t) REVERT: A 522 TYR cc_start: 0.1276 (OUTLIER) cc_final: -0.0367 (m-80) REVERT: A 536 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6030 (mp) REVERT: A 598 TYR cc_start: 0.7259 (m-80) cc_final: 0.5841 (m-80) REVERT: A 646 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.4470 (pp) REVERT: A 664 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6284 (mt) REVERT: A 685 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6205 (mm) outliers start: 49 outliers final: 27 residues processed: 143 average time/residue: 0.1610 time to fit residues: 30.9472 Evaluate side-chains 135 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 163 ASP 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 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 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 560 MET 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 664 LEU Chi-restraints excluded: chain A residue 666 LEU 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: 0.4980 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** 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: 0.5351 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5858 Z= 0.172 Angle : 0.656 15.281 7961 Z= 0.328 Chirality : 0.042 0.193 896 Planarity : 0.004 0.060 974 Dihedral : 4.590 33.241 762 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 8.15 % Allowed : 28.75 % Favored : 63.10 % 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: -0.17 (0.34), residues: 687 helix: 0.99 (0.27), residues: 411 sheet: 0.77 (1.22), residues: 17 loop : -2.06 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 668 HIS 0.004 0.001 HIS A 136 PHE 0.028 0.001 PHE A 140 TYR 0.035 0.002 TYR A 193 ARG 0.003 0.000 ARG A 170 *********************** 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 155 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 104 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6056 (mm-40) REVERT: A 411 ILE cc_start: 0.7309 (tp) cc_final: 0.7095 (mt) REVERT: A 433 ASP cc_start: 0.4342 (OUTLIER) cc_final: 0.3112 (p0) REVERT: A 437 VAL cc_start: -0.2138 (OUTLIER) cc_final: -0.2960 (m) REVERT: A 500 VAL cc_start: 0.7150 (OUTLIER) cc_final: 0.6890 (t) REVERT: A 522 TYR cc_start: 0.1258 (OUTLIER) cc_final: -0.0422 (m-80) REVERT: A 536 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.5864 (mt) REVERT: A 598 TYR cc_start: 0.7191 (m-80) cc_final: 0.5738 (m-80) REVERT: A 646 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.4214 (pp) REVERT: A 664 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6223 (mt) REVERT: A 685 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6162 (mm) outliers start: 51 outliers final: 30 residues processed: 141 average time/residue: 0.1591 time to fit residues: 29.9232 Evaluate side-chains 140 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 259 ASN 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 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 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 500 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 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 560 MET 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 664 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.0870 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5350 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5858 Z= 0.173 Angle : 0.672 15.164 7961 Z= 0.334 Chirality : 0.042 0.195 896 Planarity : 0.004 0.059 974 Dihedral : 4.555 32.967 762 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 7.67 % Allowed : 29.55 % Favored : 62.78 % 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: -0.16 (0.34), residues: 687 helix: 1.00 (0.27), residues: 412 sheet: 0.86 (1.22), residues: 17 loop : -2.06 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 668 HIS 0.004 0.001 HIS A 136 PHE 0.028 0.001 PHE A 140 TYR 0.020 0.001 TYR A 625 ARG 0.006 0.000 ARG A 571 *********************** 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 149 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 101 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.6026 (mm-40) REVERT: A 411 ILE cc_start: 0.7306 (tp) cc_final: 0.7085 (mt) REVERT: A 433 ASP cc_start: 0.4321 (OUTLIER) cc_final: 0.3084 (p0) REVERT: A 437 VAL cc_start: -0.2152 (OUTLIER) cc_final: -0.2971 (m) REVERT: A 500 VAL cc_start: 0.7171 (OUTLIER) cc_final: 0.6907 (t) REVERT: A 522 TYR cc_start: 0.1360 (OUTLIER) cc_final: -0.0331 (m-80) REVERT: A 598 TYR cc_start: 0.7173 (m-80) cc_final: 0.5667 (m-80) REVERT: A 646 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.4276 (pp) REVERT: A 664 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6182 (mt) REVERT: A 671 PHE cc_start: 0.7394 (t80) cc_final: 0.6961 (t80) REVERT: A 685 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6184 (mm) outliers start: 48 outliers final: 30 residues processed: 137 average time/residue: 0.1536 time to fit residues: 28.4391 Evaluate side-chains 136 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 259 ASN 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 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 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 500 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 529 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 574 LEU 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 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET 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: 0.2980 chunk 41 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5361 moved from start: 0.2014 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= 0.179 Angle : 0.675 15.331 7961 Z= 0.336 Chirality : 0.042 0.194 896 Planarity : 0.004 0.060 974 Dihedral : 4.538 33.118 762 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.51 % Allowed : 28.91 % 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: -0.15 (0.34), residues: 687 helix: 1.01 (0.27), residues: 412 sheet: 0.82 (1.22), residues: 17 loop : -2.07 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 668 HIS 0.003 0.001 HIS A 362 PHE 0.028 0.001 PHE A 140 TYR 0.018 0.001 TYR A 625 ARG 0.005 0.000 ARG A 571 *********************** 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 146 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 99 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6939 (t) REVERT: A 411 ILE cc_start: 0.7309 (tp) cc_final: 0.7087 (mt) REVERT: A 433 ASP cc_start: 0.4225 (OUTLIER) cc_final: 0.2914 (p0) REVERT: A 437 VAL cc_start: -0.2104 (OUTLIER) cc_final: -0.2942 (m) REVERT: A 500 VAL cc_start: 0.7211 (OUTLIER) cc_final: 0.6939 (t) REVERT: A 522 TYR cc_start: 0.1133 (OUTLIER) cc_final: -0.0484 (m-80) REVERT: A 536 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6025 (mt) REVERT: A 598 TYR cc_start: 0.7089 (m-80) cc_final: 0.5617 (m-80) REVERT: A 646 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.4239 (pp) REVERT: A 664 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6204 (mt) REVERT: A 671 PHE cc_start: 0.7404 (t80) cc_final: 0.6925 (t80) REVERT: A 685 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6199 (mm) outliers start: 47 outliers final: 33 residues processed: 133 average time/residue: 0.1627 time to fit residues: 29.3368 Evaluate side-chains 137 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 95 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 259 ASN 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 488 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 500 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 529 ILE 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 646 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET 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: 30.0000 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 583 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5858 Z= 0.246 Angle : 0.749 16.073 7961 Z= 0.377 Chirality : 0.044 0.188 896 Planarity : 0.005 0.061 974 Dihedral : 4.768 33.834 762 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 6.87 % Allowed : 29.55 % 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: -0.42 (0.33), residues: 687 helix: 0.77 (0.27), residues: 417 sheet: 0.65 (1.20), residues: 17 loop : -2.18 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 479 HIS 0.005 0.001 HIS A 362 PHE 0.027 0.001 PHE A 672 TYR 0.025 0.002 TYR A 193 ARG 0.005 0.000 ARG A 571 *********************** 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 147 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6969 (t) REVERT: A 411 ILE cc_start: 0.7384 (tp) cc_final: 0.7160 (mt) REVERT: A 427 ILE cc_start: 0.8069 (mm) cc_final: 0.7719 (mp) REVERT: A 433 ASP cc_start: 0.4343 (OUTLIER) cc_final: 0.2863 (p0) REVERT: A 437 VAL cc_start: -0.2161 (OUTLIER) cc_final: -0.3131 (m) REVERT: A 522 TYR cc_start: 0.1198 (OUTLIER) cc_final: -0.0458 (m-80) REVERT: A 598 TYR cc_start: 0.7052 (m-80) cc_final: 0.5626 (m-80) REVERT: A 664 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6295 (mt) REVERT: A 671 PHE cc_start: 0.7559 (t80) cc_final: 0.6919 (t80) REVERT: A 685 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6263 (mm) outliers start: 43 outliers final: 31 residues processed: 136 average time/residue: 0.1504 time to fit residues: 27.6277 Evaluate side-chains 140 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 ASP 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 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 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 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 652 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET 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: 1.9990 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 0.0270 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5858 Z= 0.237 Angle : 0.767 16.105 7961 Z= 0.382 Chirality : 0.045 0.194 896 Planarity : 0.005 0.061 974 Dihedral : 4.785 33.362 762 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.23 % Allowed : 30.35 % Favored : 63.42 % 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: -0.47 (0.33), residues: 687 helix: 0.80 (0.27), residues: 407 sheet: 0.74 (1.21), residues: 17 loop : -2.21 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 479 HIS 0.005 0.001 HIS A 366 PHE 0.029 0.001 PHE A 672 TYR 0.027 0.002 TYR A 193 ARG 0.004 0.000 ARG A 58 ********************** 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 140 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 101 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.7175 (OUTLIER) cc_final: 0.6945 (t) REVERT: A 411 ILE cc_start: 0.7374 (tp) cc_final: 0.7151 (mt) REVERT: A 433 ASP cc_start: 0.4145 (OUTLIER) cc_final: 0.2776 (p0) REVERT: A 437 VAL cc_start: -0.2128 (OUTLIER) cc_final: -0.3131 (m) REVERT: A 522 TYR cc_start: 0.1159 (OUTLIER) cc_final: -0.0470 (m-80) REVERT: A 598 TYR cc_start: 0.7032 (m-80) cc_final: 0.5599 (m-80) REVERT: A 664 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6276 (mt) REVERT: A 671 PHE cc_start: 0.7656 (t80) cc_final: 0.7120 (t80) REVERT: A 685 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6262 (mm) REVERT: A 690 SER cc_start: 0.7759 (t) cc_final: 0.7056 (p) outliers start: 39 outliers final: 31 residues processed: 129 average time/residue: 0.1551 time to fit residues: 27.1235 Evaluate side-chains 137 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 259 ASN 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 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 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 536 LEU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 669 MET 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: 0.0870 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 583 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.239103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.204546 restraints weight = 10552.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.208592 restraints weight = 5540.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.210986 restraints weight = 3697.231| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5858 Z= 0.221 Angle : 0.753 16.694 7961 Z= 0.375 Chirality : 0.044 0.202 896 Planarity : 0.004 0.060 974 Dihedral : 4.747 33.276 762 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 6.39 % Allowed : 30.35 % Favored : 63.26 % 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: -0.41 (0.33), residues: 687 helix: 0.85 (0.27), residues: 405 sheet: 0.81 (1.19), residues: 17 loop : -2.18 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 668 HIS 0.005 0.001 HIS A 366 PHE 0.026 0.001 PHE A 140 TYR 0.024 0.002 TYR A 193 ARG 0.004 0.000 ARG A 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1535.81 seconds wall clock time: 28 minutes 39.70 seconds (1719.70 seconds total)