Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 12:00:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/08_2023/7wro_32734.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/08_2023/7wro_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_32734/08_2023/7wro_32734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/08_2023/7wro_32734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/08_2023/7wro_32734.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wro_32734/08_2023/7wro_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-1.21rc1-5044/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: 2.15, per 1000 atoms: 0.68 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: 1.11 Conformation dependent library (CDL) restraints added in 442.4 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: 0.30 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: 0.69 Time building geometry restraints manager: 1.22 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: 2.810 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: 13.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.690 Find NCS groups from input model: 0.080 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.361 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1423 time to fit residues: 15.2079 Evaluate side-chains 74 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4788 ------------------------------------------------------------------------------- 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: 0.7383 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3256 Z= 0.185 Angle : 0.634 7.825 4420 Z= 0.329 Chirality : 0.045 0.141 470 Planarity : 0.006 0.062 579 Dihedral : 5.559 26.129 456 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.16 % 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: -1.49 (0.43), residues: 406 helix: -4.44 (0.48), residues: 32 sheet: -1.29 (0.45), residues: 125 loop : -0.21 (0.43), residues: 249 *********************** 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 85 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.369 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 0.1576 time to fit residues: 15.5398 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0313 time to fit residues: 0.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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: 0.7439 moved from start: 0.1541 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= 0.250 Angle : 0.638 11.392 4420 Z= 0.324 Chirality : 0.045 0.146 470 Planarity : 0.005 0.061 579 Dihedral : 5.228 25.059 456 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.73 % 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: -1.50 (0.43), residues: 406 helix: -4.18 (0.55), residues: 32 sheet: -1.68 (0.41), residues: 130 loop : 0.03 (0.45), residues: 244 *********************** 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 84 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.345 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.1612 time to fit residues: 15.9598 Evaluate side-chains 75 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0331 time to fit residues: 0.7146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- 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: 0.7476 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 3256 Z= 0.307 Angle : 0.645 7.293 4420 Z= 0.331 Chirality : 0.046 0.175 470 Planarity : 0.005 0.062 579 Dihedral : 5.150 22.910 456 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 3.47 % 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: -1.60 (0.44), residues: 406 helix: -4.08 (0.59), residues: 32 sheet: -1.68 (0.41), residues: 137 loop : -0.04 (0.46), residues: 237 *********************** 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 91 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.357 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 85 average time/residue: 0.1480 time to fit residues: 15.3571 Evaluate side-chains 85 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0372 time to fit residues: 1.1152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.0030 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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: 0.7409 moved from start: 0.1926 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= 0.176 Angle : 0.597 8.380 4420 Z= 0.305 Chirality : 0.044 0.181 470 Planarity : 0.005 0.060 579 Dihedral : 4.854 23.074 456 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.73 % 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: -1.37 (0.44), residues: 406 helix: -3.92 (0.66), residues: 32 sheet: -1.70 (0.42), residues: 129 loop : 0.15 (0.45), residues: 245 *********************** 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 88 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.377 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 86 average time/residue: 0.1415 time to fit residues: 15.0490 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0364 time to fit residues: 0.6247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7502 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 3256 Z= 0.338 Angle : 0.670 7.001 4420 Z= 0.345 Chirality : 0.046 0.191 470 Planarity : 0.005 0.062 579 Dihedral : 5.095 23.066 456 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 3.18 % 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: -1.57 (0.44), residues: 406 helix: -3.88 (0.67), residues: 32 sheet: -1.92 (0.42), residues: 128 loop : 0.04 (0.45), residues: 246 *********************** 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 92 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.371 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.1716 time to fit residues: 17.2648 Evaluate side-chains 86 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0428 time to fit residues: 1.1707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7477 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 3256 Z= 0.291 Angle : 0.639 8.031 4420 Z= 0.333 Chirality : 0.047 0.252 470 Planarity : 0.005 0.062 579 Dihedral : 5.077 23.142 456 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.87 % 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 (0.43), residues: 406 helix: -3.82 (0.70), residues: 32 sheet: -1.81 (0.42), residues: 122 loop : -0.09 (0.44), residues: 252 *********************** 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 82 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.354 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.1765 time to fit residues: 16.7279 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0349 time to fit residues: 0.5675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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: 0.7433 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3256 Z= 0.207 Angle : 0.616 9.948 4420 Z= 0.313 Chirality : 0.046 0.223 470 Planarity : 0.005 0.061 579 Dihedral : 4.827 22.765 456 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 2.02 % 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: -1.44 (0.43), residues: 406 helix: -3.84 (0.69), residues: 32 sheet: -1.51 (0.42), residues: 129 loop : -0.07 (0.44), residues: 245 *********************** 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 86 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.331 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 83 average time/residue: 0.1652 time to fit residues: 16.7075 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0687 time to fit residues: 0.6947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 39 optimal weight: 0.0980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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: 0.7407 moved from start: 0.2242 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= 0.185 Angle : 0.593 7.604 4420 Z= 0.306 Chirality : 0.045 0.215 470 Planarity : 0.005 0.058 579 Dihedral : 4.732 23.029 456 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.87 % 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: -1.24 (0.43), residues: 406 helix: -3.80 (0.71), residues: 32 sheet: -1.36 (0.44), residues: 112 loop : -0.05 (0.43), residues: 262 *********************** 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 84 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.318 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 81 average time/residue: 0.1685 time to fit residues: 16.4896 Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0614 time to fit residues: 0.8866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.0010 chunk 13 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.1924 ------------------------------------------------------------------------------- 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: 0.7350 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3256 Z= 0.149 Angle : 0.572 7.185 4420 Z= 0.296 Chirality : 0.044 0.209 470 Planarity : 0.005 0.056 579 Dihedral : 4.540 22.801 456 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.87 % 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: -1.09 (0.43), residues: 406 helix: -3.88 (0.67), residues: 32 sheet: -1.14 (0.45), residues: 112 loop : 0.02 (0.42), residues: 262 ********************** 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 81 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.375 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.1615 time to fit residues: 15.2198 Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0437 time to fit residues: 0.6193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.2334 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.148906 restraints weight = 4231.751| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.21 r_work: 0.3651 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3256 Z= 0.147 Angle : 0.564 7.222 4420 Z= 0.293 Chirality : 0.045 0.225 470 Planarity : 0.005 0.055 579 Dihedral : 4.444 22.427 456 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.43), residues: 406 helix: -3.90 (0.65), residues: 32 sheet: -0.98 (0.46), residues: 112 loop : 0.05 (0.43), residues: 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.54 seconds wall clock time: 24 minutes 52.71 seconds (1492.71 seconds total)