Starting phenix.real_space_refine on Thu Nov 14 05:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/11_2024/8c02_16353.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/11_2024/8c02_16353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/11_2024/8c02_16353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/11_2024/8c02_16353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/11_2024/8c02_16353.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/11_2024/8c02_16353.cif" } resolution = 4.09 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= 0.027 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 31 5.16 5 C 2767 2.51 5 N 695 2.21 5 O 749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4242 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 3.14, per 1000 atoms: 0.74 Number of scatterers: 4242 At special positions: 0 Unit cell: (76.818, 100.254, 72.912, 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 31 16.00 O 749 8.00 N 695 7.00 C 2767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " 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: 1.11 Conformation dependent library (CDL) restraints added in 529.1 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 72.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.897A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 127 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.077A pdb=" N VAL A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' Processing helix chain 'A' and resid 288 through 305 removed outlier: 3.856A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 338 through 367 removed outlier: 3.695A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 393 Processing helix chain 'A' and resid 451 through 483 removed outlier: 3.642A pdb=" N VAL A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 519 through 546 Processing helix chain 'B' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.523A pdb=" N VAL B 14 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 37 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET B 36 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA B 52 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.523A pdb=" N VAL B 14 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS B 101 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR B 112 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 103 " --> pdb=" O TYR B 110 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1014 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: 1.22 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1312 1.34 - 1.46: 1032 1.46 - 1.58: 1939 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 4335 Sorted by residual: bond pdb=" N MET A 288 " pdb=" CA MET A 288 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.25e-02 6.40e+03 8.87e+00 bond pdb=" N TYR A 318 " pdb=" CA TYR A 318 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.32e-02 5.74e+03 5.40e+00 bond pdb=" CG GLN A 93 " pdb=" CD GLN A 93 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.31e+00 bond pdb=" CG1 ILE A 136 " pdb=" CD1 ILE A 136 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CG LEU A 222 " pdb=" CD1 LEU A 222 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 4330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5701 1.98 - 3.97: 149 3.97 - 5.95: 33 5.95 - 7.94: 12 7.94 - 9.92: 3 Bond angle restraints: 5898 Sorted by residual: angle pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sigma weight residual 114.10 121.78 -7.68 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA GLU A 486 " pdb=" CB GLU A 486 " pdb=" CG GLU A 486 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" N GLN A 93 " pdb=" CA GLN A 93 " pdb=" CB GLN A 93 " ideal model delta sigma weight residual 110.28 115.21 -4.93 1.55e+00 4.16e-01 1.01e+01 angle pdb=" CB LYS A 549 " pdb=" CG LYS A 549 " pdb=" CD LYS A 549 " ideal model delta sigma weight residual 111.30 118.34 -7.04 2.30e+00 1.89e-01 9.36e+00 angle pdb=" CA GLU A 290 " pdb=" CB GLU A 290 " pdb=" CG GLU A 290 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.81e+00 ... (remaining 5893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 2262 16.19 - 32.38: 187 32.38 - 48.57: 43 48.57 - 64.76: 7 64.76 - 80.95: 5 Dihedral angle restraints: 2504 sinusoidal: 930 harmonic: 1574 Sorted by residual: dihedral pdb=" CA THR A 122 " pdb=" C THR A 122 " pdb=" N MET A 123 " pdb=" CA MET A 123 " ideal model delta harmonic sigma weight residual 180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLU B 46 " pdb=" C GLU B 46 " pdb=" N ARG B 47 " pdb=" CA ARG B 47 " ideal model delta harmonic sigma weight residual 180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA MET B 105 " pdb=" C MET B 105 " pdb=" N ALA B 106 " pdb=" CA ALA B 106 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 473 0.039 - 0.077: 164 0.077 - 0.116: 48 0.116 - 0.155: 7 0.155 - 0.193: 4 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA GLU A 290 " pdb=" N GLU A 290 " pdb=" C GLU A 290 " pdb=" CB GLU A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA GLN A 93 " pdb=" N GLN A 93 " pdb=" C GLN A 93 " pdb=" CB GLN A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB ILE B 56 " pdb=" CA ILE B 56 " pdb=" CG1 ILE B 56 " pdb=" CG2 ILE B 56 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 693 not shown) Planarity restraints: 719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 514 " -0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 515 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 29 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO B 30 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 317 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C LEU A 317 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 317 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 318 " -0.015 2.00e-02 2.50e+03 ... (remaining 716 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 718 2.76 - 3.29: 4563 3.29 - 3.83: 7381 3.83 - 4.36: 7786 4.36 - 4.90: 13676 Nonbonded interactions: 34124 Sorted by model distance: nonbonded pdb=" O CYS B 24 " pdb=" OG1 THR B 80 " model vdw 2.225 3.040 nonbonded pdb=" O VAL A 358 " pdb=" OG1 THR A 361 " model vdw 2.279 3.040 nonbonded pdb=" O ALA B 54 " pdb=" NH2 ARG B 74 " model vdw 2.298 3.120 nonbonded pdb=" N MET B 105 " pdb=" O TRP B 108 " model vdw 2.323 3.120 nonbonded pdb=" O THR A 230 " pdb=" OG1 THR A 230 " model vdw 2.339 3.040 ... (remaining 34119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 0.057 4335 Z= 0.259 Angle : 0.832 9.920 5898 Z= 0.419 Chirality : 0.045 0.193 696 Planarity : 0.007 0.083 719 Dihedral : 13.159 80.949 1497 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.44 % Allowed : 0.00 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.35), residues: 541 helix: 2.10 (0.26), residues: 367 sheet: -1.31 (0.64), residues: 39 loop : -1.40 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 38 HIS 0.002 0.001 HIS A 32 PHE 0.016 0.002 PHE A 530 TYR 0.030 0.002 TYR A 29 ARG 0.007 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8755 (t80) cc_final: 0.8459 (t80) REVERT: A 36 THR cc_start: 0.9349 (m) cc_final: 0.9145 (t) REVERT: A 111 MET cc_start: 0.8545 (tpt) cc_final: 0.8277 (mmm) REVERT: A 184 THR cc_start: 0.9334 (m) cc_final: 0.8956 (t) REVERT: A 290 GLU cc_start: 0.8139 (pm20) cc_final: 0.7931 (pm20) REVERT: A 312 MET cc_start: 0.8837 (tpt) cc_final: 0.8058 (tpp) REVERT: A 473 ASP cc_start: 0.9390 (t70) cc_final: 0.9177 (t0) REVERT: A 536 ILE cc_start: 0.8342 (mm) cc_final: 0.8104 (mm) REVERT: B 20 LEU cc_start: 0.8822 (tt) cc_final: 0.8434 (mt) REVERT: B 70 PHE cc_start: 0.7802 (m-10) cc_final: 0.7413 (m-80) REVERT: B 92 ASP cc_start: 0.7493 (m-30) cc_final: 0.6904 (m-30) REVERT: B 119 VAL cc_start: 0.9269 (t) cc_final: 0.9062 (t) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1396 time to fit residues: 34.3744 Evaluate side-chains 159 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.0040 chunk 42 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 335 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4335 Z= 0.197 Angle : 0.654 8.460 5898 Z= 0.333 Chirality : 0.040 0.164 696 Planarity : 0.005 0.065 719 Dihedral : 4.110 15.643 590 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.36), residues: 541 helix: 2.44 (0.26), residues: 369 sheet: -0.11 (0.73), residues: 43 loop : -1.41 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 38 HIS 0.003 0.001 HIS A 32 PHE 0.007 0.001 PHE A 295 TYR 0.024 0.002 TYR A 29 ARG 0.005 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8473 (tpt) cc_final: 0.8164 (mmm) REVERT: A 179 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.8024 (mtm-85) REVERT: A 180 ILE cc_start: 0.8331 (mm) cc_final: 0.8111 (mm) REVERT: A 290 GLU cc_start: 0.8585 (pm20) cc_final: 0.8380 (pm20) REVERT: A 488 GLU cc_start: 0.7271 (tp30) cc_final: 0.7046 (tp30) REVERT: A 536 ILE cc_start: 0.8236 (mm) cc_final: 0.8016 (mm) REVERT: B 6 LEU cc_start: 0.8499 (pp) cc_final: 0.8158 (pp) REVERT: B 8 GLU cc_start: 0.6806 (mp0) cc_final: 0.5093 (mp0) REVERT: B 34 ASN cc_start: 0.8040 (m-40) cc_final: 0.7582 (m110) REVERT: B 38 TRP cc_start: 0.8246 (m100) cc_final: 0.7963 (m100) REVERT: B 70 PHE cc_start: 0.7813 (m-10) cc_final: 0.7491 (m-80) REVERT: B 92 ASP cc_start: 0.7310 (m-30) cc_final: 0.6850 (m-30) REVERT: B 108 TRP cc_start: 0.8154 (t-100) cc_final: 0.7358 (t-100) REVERT: B 115 GLN cc_start: 0.8122 (pm20) cc_final: 0.7916 (pm20) REVERT: B 117 THR cc_start: 0.8814 (p) cc_final: 0.8553 (t) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1520 time to fit residues: 38.2213 Evaluate side-chains 168 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4335 Z= 0.264 Angle : 0.660 8.940 5898 Z= 0.342 Chirality : 0.041 0.161 696 Planarity : 0.004 0.047 719 Dihedral : 3.986 17.236 590 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.22 % Allowed : 3.30 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.36), residues: 541 helix: 2.35 (0.26), residues: 370 sheet: 0.31 (0.82), residues: 44 loop : -1.64 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.009 0.001 PHE A 292 TYR 0.017 0.002 TYR B 62 ARG 0.004 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8882 (t80) cc_final: 0.8541 (t80) REVERT: A 111 MET cc_start: 0.8543 (tpt) cc_final: 0.8200 (tpp) REVERT: A 179 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8127 (ttm110) REVERT: A 180 ILE cc_start: 0.8373 (mm) cc_final: 0.8148 (mm) REVERT: A 290 GLU cc_start: 0.8599 (pm20) cc_final: 0.8362 (pm20) REVERT: A 312 MET cc_start: 0.8508 (tpp) cc_final: 0.7314 (tpp) REVERT: A 536 ILE cc_start: 0.8297 (mm) cc_final: 0.8076 (mm) REVERT: B 34 ASN cc_start: 0.8289 (m-40) cc_final: 0.7693 (m110) REVERT: B 36 MET cc_start: 0.8962 (mmm) cc_final: 0.8707 (mmm) REVERT: B 38 TRP cc_start: 0.8285 (m100) cc_final: 0.7966 (m100) REVERT: B 92 ASP cc_start: 0.7384 (m-30) cc_final: 0.6887 (m-30) REVERT: B 108 TRP cc_start: 0.8426 (t-100) cc_final: 0.7941 (t-100) REVERT: B 115 GLN cc_start: 0.8076 (pm20) cc_final: 0.7804 (pm20) REVERT: B 119 VAL cc_start: 0.8906 (m) cc_final: 0.8602 (m) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1634 time to fit residues: 38.7398 Evaluate side-chains 154 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.0000 chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 0.0970 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 478 GLN ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4335 Z= 0.185 Angle : 0.630 8.766 5898 Z= 0.321 Chirality : 0.039 0.146 696 Planarity : 0.004 0.048 719 Dihedral : 3.883 15.158 590 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.36), residues: 541 helix: 2.42 (0.26), residues: 368 sheet: 0.16 (0.85), residues: 38 loop : -1.16 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.017 0.002 HIS A 535 PHE 0.010 0.001 PHE A 530 TYR 0.013 0.001 TYR B 62 ARG 0.005 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8672 (t80) cc_final: 0.8376 (t80) REVERT: A 119 GLU cc_start: 0.8105 (pm20) cc_final: 0.7858 (pm20) REVERT: A 158 TRP cc_start: 0.8781 (m-10) cc_final: 0.8383 (m-10) REVERT: A 180 ILE cc_start: 0.8313 (mm) cc_final: 0.7943 (mm) REVERT: A 290 GLU cc_start: 0.8523 (pm20) cc_final: 0.8311 (pm20) REVERT: A 293 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8380 (ptp-110) REVERT: A 302 TYR cc_start: 0.8384 (t80) cc_final: 0.7734 (t80) REVERT: A 309 LEU cc_start: 0.8721 (mt) cc_final: 0.8335 (mt) REVERT: A 335 GLN cc_start: 0.7582 (tp40) cc_final: 0.6528 (tt0) REVERT: A 485 ILE cc_start: 0.8812 (mp) cc_final: 0.8251 (mt) REVERT: A 533 MET cc_start: 0.7592 (mmm) cc_final: 0.6919 (ttt) REVERT: A 536 ILE cc_start: 0.8192 (mm) cc_final: 0.7987 (mm) REVERT: B 34 ASN cc_start: 0.8100 (m-40) cc_final: 0.7621 (m110) REVERT: B 36 MET cc_start: 0.8942 (mmm) cc_final: 0.8702 (mmm) REVERT: B 70 PHE cc_start: 0.7580 (m-10) cc_final: 0.7378 (m-80) REVERT: B 92 ASP cc_start: 0.7468 (m-30) cc_final: 0.7059 (m-30) REVERT: B 108 TRP cc_start: 0.8425 (t-100) cc_final: 0.7866 (t-100) REVERT: B 119 VAL cc_start: 0.8824 (m) cc_final: 0.8488 (m) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1513 time to fit residues: 36.6773 Evaluate side-chains 165 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4335 Z= 0.213 Angle : 0.661 8.684 5898 Z= 0.334 Chirality : 0.039 0.142 696 Planarity : 0.004 0.053 719 Dihedral : 3.875 15.665 590 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.44 % Allowed : 4.19 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.36), residues: 541 helix: 2.38 (0.26), residues: 369 sheet: 0.35 (0.85), residues: 38 loop : -1.09 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 33 HIS 0.014 0.002 HIS A 535 PHE 0.011 0.001 PHE A 292 TYR 0.016 0.002 TYR A 64 ARG 0.004 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8699 (t80) cc_final: 0.8363 (t80) REVERT: A 29 TYR cc_start: 0.9197 (m-10) cc_final: 0.8780 (m-80) REVERT: A 30 LEU cc_start: 0.9456 (tp) cc_final: 0.9162 (tt) REVERT: A 64 TYR cc_start: 0.8754 (t80) cc_final: 0.8531 (t80) REVERT: A 111 MET cc_start: 0.8159 (mmm) cc_final: 0.7812 (mmm) REVERT: A 119 GLU cc_start: 0.8103 (pm20) cc_final: 0.7878 (pm20) REVERT: A 180 ILE cc_start: 0.8206 (mm) cc_final: 0.7934 (mm) REVERT: A 302 TYR cc_start: 0.8488 (t80) cc_final: 0.7991 (t80) REVERT: A 335 GLN cc_start: 0.7591 (tp40) cc_final: 0.6531 (tt0) REVERT: A 473 ASP cc_start: 0.9576 (t70) cc_final: 0.9168 (t0) REVERT: A 479 LEU cc_start: 0.9420 (mm) cc_final: 0.9178 (mt) REVERT: B 30 PRO cc_start: 0.9496 (Cg_exo) cc_final: 0.8908 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8356 (m-40) cc_final: 0.7869 (m110) REVERT: B 36 MET cc_start: 0.8943 (mmm) cc_final: 0.8673 (mmm) REVERT: B 46 GLU cc_start: 0.7158 (pp20) cc_final: 0.6870 (pp20) REVERT: B 72 ILE cc_start: 0.8312 (tp) cc_final: 0.8078 (tp) REVERT: B 92 ASP cc_start: 0.7363 (m-30) cc_final: 0.6968 (m-30) REVERT: B 108 TRP cc_start: 0.8619 (t-100) cc_final: 0.8368 (t-100) REVERT: B 119 VAL cc_start: 0.8854 (m) cc_final: 0.8464 (m) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 0.1523 time to fit residues: 36.2072 Evaluate side-chains 154 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4335 Z= 0.216 Angle : 0.665 8.718 5898 Z= 0.340 Chirality : 0.040 0.166 696 Planarity : 0.005 0.054 719 Dihedral : 3.926 15.055 590 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.22 % Allowed : 1.76 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.36), residues: 541 helix: 2.34 (0.26), residues: 369 sheet: 0.28 (0.79), residues: 43 loop : -1.17 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 108 HIS 0.013 0.002 HIS A 535 PHE 0.021 0.001 PHE B 70 TYR 0.019 0.001 TYR A 318 ARG 0.003 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8667 (t80) cc_final: 0.8348 (t80) REVERT: A 30 LEU cc_start: 0.9441 (tp) cc_final: 0.9145 (tt) REVERT: A 111 MET cc_start: 0.8188 (mmm) cc_final: 0.7783 (mmm) REVERT: A 119 GLU cc_start: 0.8239 (pm20) cc_final: 0.7903 (pm20) REVERT: A 180 ILE cc_start: 0.8163 (mm) cc_final: 0.7910 (mm) REVERT: A 335 GLN cc_start: 0.7796 (tp40) cc_final: 0.6807 (tt0) REVERT: A 473 ASP cc_start: 0.9592 (t70) cc_final: 0.9109 (t0) REVERT: A 495 VAL cc_start: 0.9460 (m) cc_final: 0.9202 (p) REVERT: A 533 MET cc_start: 0.7425 (mmm) cc_final: 0.7030 (ttt) REVERT: B 30 PRO cc_start: 0.9481 (Cg_exo) cc_final: 0.8826 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8321 (m-40) cc_final: 0.7804 (m110) REVERT: B 36 MET cc_start: 0.8931 (mmm) cc_final: 0.8658 (mmm) REVERT: B 72 ILE cc_start: 0.8322 (tp) cc_final: 0.8117 (tp) REVERT: B 92 ASP cc_start: 0.7460 (m-30) cc_final: 0.7241 (m-30) REVERT: B 119 VAL cc_start: 0.8841 (m) cc_final: 0.8447 (m) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1458 time to fit residues: 33.8517 Evaluate side-chains 156 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4335 Z= 0.225 Angle : 0.664 8.774 5898 Z= 0.340 Chirality : 0.040 0.170 696 Planarity : 0.005 0.058 719 Dihedral : 3.873 15.169 590 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.22 % Allowed : 1.76 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.36), residues: 541 helix: 2.21 (0.26), residues: 370 sheet: 0.10 (0.75), residues: 43 loop : -1.20 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 108 HIS 0.012 0.002 HIS A 535 PHE 0.009 0.001 PHE A 541 TYR 0.017 0.002 TYR A 318 ARG 0.004 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8572 (t80) cc_final: 0.8294 (t80) REVERT: A 30 LEU cc_start: 0.9436 (tp) cc_final: 0.9145 (tt) REVERT: A 111 MET cc_start: 0.8246 (mmm) cc_final: 0.7860 (mmm) REVERT: A 119 GLU cc_start: 0.8376 (pm20) cc_final: 0.8101 (pm20) REVERT: A 180 ILE cc_start: 0.8067 (mm) cc_final: 0.7845 (mm) REVERT: A 190 MET cc_start: 0.8781 (tmm) cc_final: 0.8520 (tmm) REVERT: A 194 GLN cc_start: 0.8272 (tt0) cc_final: 0.7683 (tt0) REVERT: A 335 GLN cc_start: 0.7764 (tp40) cc_final: 0.6868 (tt0) REVERT: A 392 PHE cc_start: 0.7368 (t80) cc_final: 0.7159 (t80) REVERT: A 495 VAL cc_start: 0.9429 (m) cc_final: 0.9170 (p) REVERT: A 533 MET cc_start: 0.7279 (mmm) cc_final: 0.7015 (ttt) REVERT: B 30 PRO cc_start: 0.9423 (Cg_exo) cc_final: 0.8795 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8337 (m-40) cc_final: 0.7873 (m110) REVERT: B 36 MET cc_start: 0.9045 (mmm) cc_final: 0.8749 (mmm) REVERT: B 72 ILE cc_start: 0.8364 (tp) cc_final: 0.8147 (tp) REVERT: B 119 VAL cc_start: 0.8833 (m) cc_final: 0.8453 (m) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1406 time to fit residues: 31.5233 Evaluate side-chains 155 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 49 optimal weight: 0.0470 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4335 Z= 0.208 Angle : 0.691 8.945 5898 Z= 0.352 Chirality : 0.041 0.181 696 Planarity : 0.005 0.059 719 Dihedral : 3.886 14.821 590 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.36), residues: 541 helix: 2.22 (0.26), residues: 369 sheet: 0.06 (0.75), residues: 43 loop : -1.13 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 42 HIS 0.011 0.002 HIS A 535 PHE 0.019 0.001 PHE A 292 TYR 0.021 0.001 TYR A 318 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8517 (t80) cc_final: 0.8294 (t80) REVERT: A 30 LEU cc_start: 0.9409 (tp) cc_final: 0.9109 (tt) REVERT: A 64 TYR cc_start: 0.8728 (t80) cc_final: 0.8430 (t80) REVERT: A 111 MET cc_start: 0.8117 (mmm) cc_final: 0.7756 (mmm) REVERT: A 119 GLU cc_start: 0.8357 (pm20) cc_final: 0.8076 (pm20) REVERT: A 190 MET cc_start: 0.8719 (tmm) cc_final: 0.8437 (tmm) REVERT: A 194 GLN cc_start: 0.8240 (tt0) cc_final: 0.7664 (tt0) REVERT: A 335 GLN cc_start: 0.7705 (tp40) cc_final: 0.6765 (tt0) REVERT: A 473 ASP cc_start: 0.9547 (t70) cc_final: 0.9250 (t0) REVERT: A 495 VAL cc_start: 0.9420 (m) cc_final: 0.9211 (p) REVERT: A 500 ASN cc_start: 0.8624 (m110) cc_final: 0.8294 (m-40) REVERT: A 533 MET cc_start: 0.7290 (mmm) cc_final: 0.7016 (ttt) REVERT: B 30 PRO cc_start: 0.9398 (Cg_exo) cc_final: 0.8924 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8248 (m-40) cc_final: 0.7804 (m110) REVERT: B 36 MET cc_start: 0.8968 (mmm) cc_final: 0.8707 (mmm) REVERT: B 39 TYR cc_start: 0.7980 (m-80) cc_final: 0.7588 (m-10) REVERT: B 72 ILE cc_start: 0.8368 (tp) cc_final: 0.8152 (tp) REVERT: B 119 VAL cc_start: 0.8821 (m) cc_final: 0.8505 (m) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1282 time to fit residues: 30.0429 Evaluate side-chains 156 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4335 Z= 0.242 Angle : 0.745 9.754 5898 Z= 0.377 Chirality : 0.041 0.179 696 Planarity : 0.005 0.077 719 Dihedral : 4.059 16.487 590 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.36), residues: 541 helix: 2.12 (0.26), residues: 370 sheet: 0.28 (0.78), residues: 43 loop : -1.21 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 470 HIS 0.010 0.002 HIS A 535 PHE 0.010 0.001 PHE A 530 TYR 0.017 0.002 TYR A 318 ARG 0.004 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8559 (t80) cc_final: 0.8286 (t80) REVERT: A 30 LEU cc_start: 0.9424 (tp) cc_final: 0.9145 (tt) REVERT: A 52 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8700 (mm-30) REVERT: A 111 MET cc_start: 0.8086 (mmm) cc_final: 0.7807 (mmm) REVERT: A 119 GLU cc_start: 0.8395 (pm20) cc_final: 0.8115 (pm20) REVERT: A 190 MET cc_start: 0.8715 (tmm) cc_final: 0.8406 (tmm) REVERT: A 194 GLN cc_start: 0.8331 (tt0) cc_final: 0.7757 (tt0) REVERT: A 335 GLN cc_start: 0.7703 (tp40) cc_final: 0.6814 (tt0) REVERT: A 495 VAL cc_start: 0.9412 (m) cc_final: 0.9172 (p) REVERT: A 533 MET cc_start: 0.7408 (mmm) cc_final: 0.7161 (ttt) REVERT: B 30 PRO cc_start: 0.9424 (Cg_exo) cc_final: 0.8820 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8347 (m-40) cc_final: 0.7828 (m110) REVERT: B 36 MET cc_start: 0.9008 (mmm) cc_final: 0.8710 (mmm) REVERT: B 39 TYR cc_start: 0.8113 (m-80) cc_final: 0.7644 (m-10) REVERT: B 72 ILE cc_start: 0.8319 (tp) cc_final: 0.8090 (tp) REVERT: B 119 VAL cc_start: 0.8809 (m) cc_final: 0.8432 (m) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1350 time to fit residues: 30.9060 Evaluate side-chains 150 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4335 Z= 0.216 Angle : 0.749 9.844 5898 Z= 0.376 Chirality : 0.041 0.190 696 Planarity : 0.005 0.061 719 Dihedral : 3.993 14.864 590 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.37), residues: 541 helix: 2.06 (0.26), residues: 370 sheet: 0.20 (0.77), residues: 43 loop : -1.21 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 38 HIS 0.011 0.002 HIS A 535 PHE 0.025 0.001 PHE A 292 TYR 0.014 0.001 TYR A 318 ARG 0.005 0.001 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8533 (t80) cc_final: 0.8311 (t80) REVERT: A 111 MET cc_start: 0.8069 (mmm) cc_final: 0.7772 (mmm) REVERT: A 119 GLU cc_start: 0.8367 (pm20) cc_final: 0.8088 (pm20) REVERT: A 190 MET cc_start: 0.8708 (tmm) cc_final: 0.8413 (tmm) REVERT: A 194 GLN cc_start: 0.8308 (tt0) cc_final: 0.7743 (tt0) REVERT: A 324 PHE cc_start: 0.7593 (m-10) cc_final: 0.7306 (m-10) REVERT: A 335 GLN cc_start: 0.7705 (tp40) cc_final: 0.6821 (tt0) REVERT: A 393 MET cc_start: 0.7654 (mmm) cc_final: 0.7370 (mmt) REVERT: A 470 TRP cc_start: 0.8353 (m100) cc_final: 0.7934 (m100) REVERT: A 495 VAL cc_start: 0.9409 (m) cc_final: 0.9174 (p) REVERT: A 533 MET cc_start: 0.7404 (mmm) cc_final: 0.7107 (ttt) REVERT: B 30 PRO cc_start: 0.9445 (Cg_exo) cc_final: 0.8942 (Cg_endo) REVERT: B 34 ASN cc_start: 0.8349 (m-40) cc_final: 0.7811 (m110) REVERT: B 36 MET cc_start: 0.9004 (mmm) cc_final: 0.8699 (mmm) REVERT: B 38 TRP cc_start: 0.7974 (m100) cc_final: 0.7550 (m-10) REVERT: B 39 TYR cc_start: 0.8132 (m-80) cc_final: 0.7808 (m-10) REVERT: B 119 VAL cc_start: 0.8832 (m) cc_final: 0.8513 (m) outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 0.1376 time to fit residues: 30.8357 Evaluate side-chains 150 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108035 restraints weight = 8768.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111522 restraints weight = 5170.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113939 restraints weight = 3570.879| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4335 Z= 0.243 Angle : 0.740 9.469 5898 Z= 0.377 Chirality : 0.041 0.185 696 Planarity : 0.004 0.059 719 Dihedral : 4.007 14.889 590 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.37), residues: 541 helix: 2.06 (0.26), residues: 370 sheet: -0.05 (0.76), residues: 43 loop : -1.17 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 470 HIS 0.010 0.002 HIS A 535 PHE 0.018 0.001 PHE A 292 TYR 0.017 0.001 TYR A 318 ARG 0.004 0.001 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1347.69 seconds wall clock time: 25 minutes 14.42 seconds (1514.42 seconds total)