Starting phenix.real_space_refine on Wed Jan 17 12:27:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/01_2024/7wro_32734.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/01_2024/7wro_32734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/01_2024/7wro_32734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/01_2024/7wro_32734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/01_2024/7wro_32734.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/01_2024/7wro_32734.pdb" } resolution = 3.4 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= -0.000 sd= 0.024 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 14 5.16 5 C 2004 2.51 5 N 541 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "L ASP 74": "OD1" <-> "OD2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 102": "OD1" <-> "OD2" Residue "L ASP 113": "OD1" <-> "OD2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 389": "OD1" <-> "OD2" Residue "R PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 406": "OE1" <-> "OE2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 465": "OE1" <-> "OE2" Residue "R TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3179 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 916 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 796 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "R" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1467 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Time building chain proxies: 2.26, per 1000 atoms: 0.71 Number of scatterers: 3179 At special positions: 0 Unit cell: (68.48, 82.39, 84.53, 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 14 16.00 O 620 8.00 N 541 7.00 C 2004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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: 1.14 Conformation dependent library (CDL) restraints added in 636.9 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.613A pdb=" N LYS H 84 " --> pdb=" O ASP H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.894A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR H 110 " --> pdb=" O ASP H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 390 removed outlier: 3.622A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 408 removed outlier: 4.009A pdb=" N VAL R 407 " --> pdb=" O GLY R 404 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 404 through 408' Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.878A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.680A pdb=" N SER H 97 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 77 through 79 removed outlier: 5.446A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'L' and resid 66 through 67 removed outlier: 3.703A pdb=" N ALA L 105 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 86 through 88 removed outlier: 3.971A pdb=" N SER L 86 " --> pdb=" O SER L 93 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 93 " --> pdb=" O SER L 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 110 through 113 Processing sheet with id=AA7, first strand: chain 'R' and resid 396 through 402 removed outlier: 3.755A pdb=" N SER R 514 " --> pdb=" O TYR R 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 168 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: 0.72 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1037 1.34 - 1.47: 904 1.47 - 1.60: 1298 1.60 - 1.73: 0 1.73 - 1.86: 17 Bond restraints: 3256 Sorted by residual: bond pdb=" C TYR R 505 " pdb=" N GLN R 506 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.15e+00 bond pdb=" CG1 ILE R 402 " pdb=" CD1 ILE R 402 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 bond pdb=" CA ARG R 509 " pdb=" CB ARG R 509 " ideal model delta sigma weight residual 1.527 1.502 0.026 1.30e-02 5.92e+03 3.87e+00 bond pdb=" CB TRP L 56 " pdb=" CG TRP L 56 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.10e+00 bond pdb=" N THR H 124 " pdb=" CA THR H 124 " ideal model delta sigma weight residual 1.454 1.429 0.025 1.42e-02 4.96e+03 3.02e+00 ... (remaining 3251 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 96 106.81 - 113.61: 1668 113.61 - 120.42: 1228 120.42 - 127.22: 1397 127.22 - 134.02: 31 Bond angle restraints: 4420 Sorted by residual: angle pdb=" CB LYS H 32 " pdb=" CG LYS H 32 " pdb=" CD LYS H 32 " ideal model delta sigma weight residual 111.30 123.47 -12.17 2.30e+00 1.89e-01 2.80e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 125.41 -11.01 2.30e+00 1.89e-01 2.29e+01 angle pdb=" N SER L 70 " pdb=" CA SER L 70 " pdb=" C SER L 70 " ideal model delta sigma weight residual 110.80 101.57 9.23 2.13e+00 2.20e-01 1.88e+01 angle pdb=" C LEU L 69 " pdb=" N SER L 70 " pdb=" CA SER L 70 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" CA LEU R 368 " pdb=" CB LEU R 368 " pdb=" CG LEU R 368 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.44e+01 ... (remaining 4415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 1660 15.04 - 30.09: 192 30.09 - 45.13: 51 45.13 - 60.18: 8 60.18 - 75.22: 4 Dihedral angle restraints: 1915 sinusoidal: 736 harmonic: 1179 Sorted by residual: dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.32 67.68 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA GLY L 71 " pdb=" C GLY L 71 " pdb=" N ASN L 72 " pdb=" CA ASN L 72 " ideal model delta harmonic sigma weight residual 180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual -86.00 -132.02 46.02 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 1912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 449 0.126 - 0.252: 20 0.252 - 0.378: 0 0.378 - 0.504: 0 0.504 - 0.630: 1 Chirality restraints: 470 Sorted by residual: chirality pdb=" CB ILE R 468 " pdb=" CA ILE R 468 " pdb=" CG1 ILE R 468 " pdb=" CG2 ILE R 468 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.63 2.00e-01 2.50e+01 9.92e+00 chirality pdb=" CB VAL R 407 " pdb=" CA VAL R 407 " pdb=" CG1 VAL R 407 " pdb=" CG2 VAL R 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE R 402 " pdb=" CA ILE R 402 " pdb=" CG1 ILE R 402 " pdb=" CG2 ILE R 402 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 467 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 79 " -0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO L 80 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO R 463 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 94 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C LEU L 94 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU L 94 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA L 95 " 0.016 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1066 2.83 - 3.35: 2712 3.35 - 3.86: 5241 3.86 - 4.38: 6124 4.38 - 4.90: 10698 Nonbonded interactions: 25841 Sorted by model distance: nonbonded pdb=" OG SER L 46 " pdb=" OD1 ASP L 113 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR L 24 " pdb=" O VAL L 42 " model vdw 2.323 2.440 nonbonded pdb=" O PHE H 48 " pdb=" NH2 ARG H 91 " model vdw 2.328 2.520 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.330 2.440 nonbonded pdb=" OD1 ASP L 103 " pdb=" OH TYR L 107 " model vdw 2.342 2.440 ... (remaining 25836 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 individual isotropic 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.880 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 3256 Z= 0.513 Angle : 1.108 13.264 4420 Z= 0.599 Chirality : 0.067 0.630 470 Planarity : 0.008 0.079 579 Dihedral : 13.649 75.223 1156 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.94 (0.42), residues: 406 helix: -4.41 (0.54), residues: 32 sheet: -1.98 (0.45), residues: 113 loop : -0.45 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 56 HIS 0.001 0.000 HIS H 22 PHE 0.021 0.004 PHE H 87 TYR 0.018 0.002 TYR R 380 ARG 0.018 0.002 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.6641 (tpp) cc_final: 0.6024 (tpp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1432 time to fit residues: 15.3162 Evaluate side-chains 74 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3256 Z= 0.191 Angle : 0.649 8.213 4420 Z= 0.338 Chirality : 0.046 0.142 470 Planarity : 0.006 0.062 579 Dihedral : 5.644 26.240 456 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.16 % Allowed : 10.98 % Favored : 87.86 % 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: -1.54 (0.43), residues: 406 helix: -4.43 (0.49), residues: 32 sheet: -1.27 (0.46), residues: 120 loop : -0.31 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 56 HIS 0.000 0.000 HIS L 55 PHE 0.019 0.001 PHE R 486 TYR 0.013 0.001 TYR R 380 ARG 0.005 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.321 Fit side-chains REVERT: R 417 LYS cc_start: 0.7753 (tppt) cc_final: 0.6998 (ttpt) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.1504 time to fit residues: 14.8184 Evaluate side-chains 76 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain R residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3256 Z= 0.247 Angle : 0.648 11.118 4420 Z= 0.329 Chirality : 0.045 0.149 470 Planarity : 0.005 0.062 579 Dihedral : 5.279 25.162 456 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.60 % Allowed : 16.47 % Favored : 80.92 % 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: -1.54 (0.44), residues: 406 helix: -4.16 (0.56), residues: 32 sheet: -1.59 (0.41), residues: 136 loop : -0.03 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.001 0.001 HIS L 55 PHE 0.017 0.001 PHE H 87 TYR 0.012 0.001 TYR R 380 ARG 0.005 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.357 Fit side-chains REVERT: R 417 LYS cc_start: 0.7858 (tppt) cc_final: 0.7122 (ttpt) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.1503 time to fit residues: 15.0855 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain R residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0040 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3256 Z= 0.278 Angle : 0.623 6.747 4420 Z= 0.324 Chirality : 0.046 0.167 470 Planarity : 0.005 0.061 579 Dihedral : 5.143 23.045 456 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.91 % Allowed : 15.61 % Favored : 79.48 % 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: -1.56 (0.44), residues: 406 helix: -4.04 (0.61), residues: 32 sheet: -1.68 (0.42), residues: 137 loop : -0.00 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.043 0.002 PHE H 87 TYR 0.012 0.001 TYR L 112 ARG 0.005 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.361 Fit side-chains REVERT: H 57 ARG cc_start: 0.7819 (ptt90) cc_final: 0.7580 (ptt90) REVERT: R 417 LYS cc_start: 0.7963 (tppt) cc_final: 0.7202 (ttpt) outliers start: 17 outliers final: 15 residues processed: 89 average time/residue: 0.1438 time to fit residues: 15.6533 Evaluate side-chains 89 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3256 Z= 0.178 Angle : 0.598 8.081 4420 Z= 0.306 Chirality : 0.044 0.208 470 Planarity : 0.005 0.061 579 Dihedral : 4.808 23.038 456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.20 % Allowed : 15.61 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.44), residues: 406 helix: -3.91 (0.67), residues: 32 sheet: -1.74 (0.42), residues: 129 loop : 0.14 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.028 0.001 PHE H 87 TYR 0.011 0.001 TYR R 380 ARG 0.005 0.000 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.354 Fit side-chains REVERT: H 87 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: R 417 LYS cc_start: 0.7927 (tppt) cc_final: 0.7175 (ttpt) REVERT: R 434 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7527 (pt) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.1332 time to fit residues: 14.4711 Evaluate side-chains 91 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.0570 chunk 28 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3256 Z= 0.236 Angle : 0.605 6.931 4420 Z= 0.313 Chirality : 0.045 0.202 470 Planarity : 0.005 0.061 579 Dihedral : 4.812 22.258 456 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 6.65 % Allowed : 15.61 % Favored : 77.75 % 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: -1.47 (0.44), residues: 406 helix: -3.88 (0.67), residues: 32 sheet: -1.56 (0.43), residues: 129 loop : -0.07 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.026 0.001 PHE H 87 TYR 0.011 0.001 TYR L 112 ARG 0.006 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.364 Fit side-chains REVERT: H 81 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7454 (t0) REVERT: R 417 LYS cc_start: 0.7990 (tppt) cc_final: 0.7243 (ttpt) outliers start: 23 outliers final: 19 residues processed: 85 average time/residue: 0.1570 time to fit residues: 16.0999 Evaluate side-chains 93 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 35 GLN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 11 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3256 Z= 0.163 Angle : 0.587 7.511 4420 Z= 0.303 Chirality : 0.044 0.223 470 Planarity : 0.005 0.061 579 Dihedral : 4.632 22.692 456 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.07 % Allowed : 16.18 % Favored : 77.75 % 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: -1.32 (0.44), residues: 406 helix: -3.82 (0.70), residues: 32 sheet: -1.54 (0.43), residues: 123 loop : 0.05 (0.44), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.027 0.001 PHE H 87 TYR 0.011 0.001 TYR R 380 ARG 0.006 0.000 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.373 Fit side-chains REVERT: H 81 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7576 (t0) REVERT: R 417 LYS cc_start: 0.7960 (tppt) cc_final: 0.7191 (ttpt) REVERT: R 434 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7531 (pt) outliers start: 21 outliers final: 17 residues processed: 87 average time/residue: 0.1398 time to fit residues: 15.0101 Evaluate side-chains 93 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3256 Z= 0.264 Angle : 0.622 7.340 4420 Z= 0.320 Chirality : 0.045 0.226 470 Planarity : 0.005 0.062 579 Dihedral : 4.782 21.974 456 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 6.36 % Allowed : 16.18 % Favored : 77.46 % 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: -1.35 (0.44), residues: 406 helix: -3.85 (0.68), residues: 32 sheet: -1.47 (0.43), residues: 129 loop : 0.02 (0.45), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 56 HIS 0.002 0.001 HIS H 22 PHE 0.026 0.001 PHE H 87 TYR 0.013 0.001 TYR L 112 ARG 0.006 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.358 Fit side-chains REVERT: H 81 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7691 (t0) REVERT: R 417 LYS cc_start: 0.8064 (tppt) cc_final: 0.7216 (ttmt) outliers start: 22 outliers final: 21 residues processed: 88 average time/residue: 0.1490 time to fit residues: 15.9488 Evaluate side-chains 98 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3256 Z= 0.180 Angle : 0.592 7.644 4420 Z= 0.303 Chirality : 0.044 0.216 470 Planarity : 0.005 0.062 579 Dihedral : 4.593 22.709 456 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.07 % Allowed : 17.05 % Favored : 76.88 % 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: -1.22 (0.44), residues: 406 helix: -3.78 (0.71), residues: 32 sheet: -1.47 (0.43), residues: 123 loop : 0.13 (0.44), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 56 HIS 0.000 0.000 HIS L 55 PHE 0.020 0.001 PHE H 87 TYR 0.011 0.001 TYR R 380 ARG 0.008 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.328 Fit side-chains REVERT: H 81 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7608 (t0) REVERT: R 417 LYS cc_start: 0.8021 (tppt) cc_final: 0.7266 (ttpt) outliers start: 21 outliers final: 19 residues processed: 92 average time/residue: 0.1500 time to fit residues: 16.8497 Evaluate side-chains 99 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3256 Z= 0.169 Angle : 0.579 7.121 4420 Z= 0.299 Chirality : 0.044 0.215 470 Planarity : 0.005 0.061 579 Dihedral : 4.518 22.492 456 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.07 % Allowed : 17.05 % Favored : 76.88 % 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: -1.11 (0.44), residues: 406 helix: -3.85 (0.68), residues: 32 sheet: -1.33 (0.43), residues: 123 loop : 0.18 (0.44), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.016 0.001 PHE H 87 TYR 0.011 0.001 TYR R 380 ARG 0.007 0.000 ARG H 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.374 Fit side-chains REVERT: H 81 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7665 (t0) REVERT: R 417 LYS cc_start: 0.8039 (tppt) cc_final: 0.7194 (ttmt) outliers start: 21 outliers final: 19 residues processed: 93 average time/residue: 0.1735 time to fit residues: 19.5195 Evaluate side-chains 102 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.4980 chunk 36 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.168248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145763 restraints weight = 4237.159| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.21 r_work: 0.3621 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3256 Z= 0.171 Angle : 0.576 7.064 4420 Z= 0.296 Chirality : 0.044 0.215 470 Planarity : 0.005 0.061 579 Dihedral : 4.469 22.726 456 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.07 % Allowed : 17.92 % Favored : 76.01 % 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: -1.04 (0.44), residues: 406 helix: -3.90 (0.65), residues: 32 sheet: -1.24 (0.44), residues: 123 loop : 0.21 (0.44), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.015 0.001 PHE H 87 TYR 0.014 0.001 TYR R 421 ARG 0.007 0.000 ARG H 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1395.73 seconds wall clock time: 26 minutes 11.47 seconds (1571.47 seconds total)