Starting phenix.real_space_refine on Fri Apr 5 13:09:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p7l_17536/04_2024/8p7l_17536_updated.pdb" } resolution = 2.1 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= 0.002 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 12 5.16 5 C 1635 2.51 5 N 429 2.21 5 O 492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 282": "OD1" <-> "OD2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "J TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2568 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 194 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain breaks: 1 Chain: "J" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2300 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 270} Chain breaks: 2 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'WD9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Time building chain proxies: 1.94, per 1000 atoms: 0.76 Number of scatterers: 2568 At special positions: 0 Unit cell: (59.85, 77.805, 68.4, 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 12 16.00 O 492 8.00 N 429 7.00 C 1635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.04 Conformation dependent library (CDL) restraints added in 442.4 milliseconds 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 586 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 1 sheets defined 36.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'H' and resid 280 through 285 Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'J' and resid 57 through 66 Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 192 through 208 removed outlier: 4.411A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE J 202 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 229 removed outlier: 3.938A pdb=" N LEU J 222 " --> pdb=" O ASP J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 77 through 83 removed outlier: 6.437A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE J 87 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN J 36 " --> pdb=" O ASP J 31 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 171 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: 0.57 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 808 1.34 - 1.46: 560 1.46 - 1.58: 1202 1.58 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 2589 Sorted by residual: bond pdb=" C12 WD9 J 401 " pdb=" C4 WD9 J 401 " ideal model delta sigma weight residual 1.368 1.393 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" CB PHE J 81 " pdb=" CG PHE J 81 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.09e+00 bond pdb=" C5 WD9 J 401 " pdb=" N10 WD9 J 401 " ideal model delta sigma weight residual 1.318 1.298 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C9 WD9 J 401 " pdb=" N10 WD9 J 401 " ideal model delta sigma weight residual 1.340 1.359 -0.019 2.00e-02 2.50e+03 8.88e-01 bond pdb=" C4 WD9 J 401 " pdb=" C5 WD9 J 401 " ideal model delta sigma weight residual 1.389 1.407 -0.018 2.00e-02 2.50e+03 8.49e-01 ... (remaining 2584 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.33: 67 105.33 - 112.49: 1323 112.49 - 119.65: 869 119.65 - 126.80: 1209 126.80 - 133.96: 41 Bond angle restraints: 3509 Sorted by residual: angle pdb=" C12 WD9 J 401 " pdb=" C4 WD9 J 401 " pdb=" C2 WD9 J 401 " ideal model delta sigma weight residual 93.42 126.33 -32.91 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C2 WD9 J 401 " pdb=" C4 WD9 J 401 " pdb=" C5 WD9 J 401 " ideal model delta sigma weight residual 158.61 126.24 32.37 3.00e+00 1.11e-01 1.16e+02 angle pdb=" N10 WD9 J 401 " pdb=" C9 WD9 J 401 " pdb=" N13 WD9 J 401 " ideal model delta sigma weight residual 89.51 119.33 -29.82 3.00e+00 1.11e-01 9.88e+01 angle pdb=" N13 WD9 J 401 " pdb=" C9 WD9 J 401 " pdb=" N8 WD9 J 401 " ideal model delta sigma weight residual 144.20 120.75 23.45 3.00e+00 1.11e-01 6.11e+01 angle pdb=" N6 WD9 J 401 " pdb=" C7 WD9 J 401 " pdb=" O26 WD9 J 401 " ideal model delta sigma weight residual 112.53 119.33 -6.80 3.00e+00 1.11e-01 5.13e+00 ... (remaining 3504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 1491 34.06 - 68.13: 38 68.13 - 102.19: 7 102.19 - 136.25: 1 136.25 - 170.32: 1 Dihedral angle restraints: 1538 sinusoidal: 631 harmonic: 907 Sorted by residual: dihedral pdb=" C15 WD9 J 401 " pdb=" C14 WD9 J 401 " pdb=" N13 WD9 J 401 " pdb=" C9 WD9 J 401 " ideal model delta sinusoidal sigma weight residual 136.76 -52.92 -170.32 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C28 WD9 J 401 " pdb=" C29 WD9 J 401 " pdb=" C30 WD9 J 401 " pdb=" N31 WD9 J 401 " ideal model delta sinusoidal sigma weight residual -52.95 59.73 -112.68 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CB GLU J 126 " pdb=" CG GLU J 126 " pdb=" CD GLU J 126 " pdb=" OE1 GLU J 126 " ideal model delta sinusoidal sigma weight residual 0.00 86.38 -86.38 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 1535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 204 0.027 - 0.054: 106 0.054 - 0.081: 45 0.081 - 0.109: 27 0.109 - 0.136: 5 Chirality restraints: 387 Sorted by residual: chirality pdb=" CA ILE J 255 " pdb=" N ILE J 255 " pdb=" C ILE J 255 " pdb=" CB ILE J 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE J 74 " pdb=" N ILE J 74 " pdb=" C ILE J 74 " pdb=" CB ILE J 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 384 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 279 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO H 280 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 280 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 280 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 210 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO J 211 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 211 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 211 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 71 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO J 72 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 72 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 72 " -0.016 5.00e-02 4.00e+02 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 409 2.76 - 3.29: 2635 3.29 - 3.83: 4600 3.83 - 4.36: 5720 4.36 - 4.90: 9242 Nonbonded interactions: 22606 Sorted by model distance: nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR J 294 " pdb=" O HOH J 501 " model vdw 2.228 2.440 nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 402 " model vdw 2.260 2.440 nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 502 " model vdw 2.266 2.440 nonbonded pdb=" O HOH J 514 " pdb=" O HOH J 533 " model vdw 2.269 2.440 ... (remaining 22601 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: 1.400 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: 7.010 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.480 Find NCS groups from input model: 0.060 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:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.003 0.025 2589 Z= 0.208 Angle : 1.182 32.910 3509 Z= 0.458 Chirality : 0.043 0.136 387 Planarity : 0.005 0.040 445 Dihedral : 17.399 170.316 952 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.95 % Favored : 96.72 % Rotamer: Outliers : 1.11 % Allowed : 18.89 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.23 (0.47), residues: 305 helix: 0.13 (0.49), residues: 109 sheet: -0.93 (1.05), residues: 20 loop : -0.14 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.015 0.002 PHE J 91 TYR 0.011 0.002 TYR J 127 ARG 0.008 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.282 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 1.3105 time to fit residues: 68.5189 Evaluate side-chains 49 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 242 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.212 Angle : 0.581 7.323 3509 Z= 0.287 Chirality : 0.043 0.126 387 Planarity : 0.005 0.039 445 Dihedral : 11.180 177.301 347 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.93 % Favored : 95.74 % Rotamer: Outliers : 2.59 % Allowed : 15.19 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.21 (0.47), residues: 305 helix: 0.13 (0.48), residues: 109 sheet: -0.69 (1.09), residues: 18 loop : -0.14 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.022 0.002 PHE J 81 TYR 0.008 0.001 TYR H 248 ARG 0.005 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.294 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 1.2092 time to fit residues: 62.0463 Evaluate side-chains 48 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.216 Angle : 0.578 6.838 3509 Z= 0.288 Chirality : 0.043 0.126 387 Planarity : 0.005 0.039 445 Dihedral : 10.888 173.898 346 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 4.07 % Allowed : 12.59 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.26 (0.47), residues: 305 helix: 0.07 (0.48), residues: 110 sheet: -0.37 (1.00), residues: 22 loop : -0.21 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.013 0.002 PHE J 91 TYR 0.009 0.002 TYR H 248 ARG 0.005 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.324 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 1.1350 time to fit residues: 59.4828 Evaluate side-chains 45 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.0030 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2589 Z= 0.171 Angle : 0.537 5.711 3509 Z= 0.269 Chirality : 0.042 0.127 387 Planarity : 0.005 0.039 445 Dihedral : 10.748 174.590 345 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 2.96 % Allowed : 14.44 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.24 (0.47), residues: 305 helix: 0.17 (0.47), residues: 117 sheet: -0.48 (1.09), residues: 20 loop : -0.26 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.002 0.001 HIS J 71 PHE 0.012 0.001 PHE J 91 TYR 0.014 0.002 TYR J 27 ARG 0.006 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.2226 time to fit residues: 61.4575 Evaluate side-chains 44 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.199 Angle : 0.559 5.928 3509 Z= 0.280 Chirality : 0.043 0.127 387 Planarity : 0.005 0.038 445 Dihedral : 10.812 175.083 345 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 3.33 % Allowed : 14.07 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.11 (0.47), residues: 305 helix: 0.17 (0.48), residues: 110 sheet: -0.34 (1.00), residues: 22 loop : -0.08 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.026 0.002 PHE J 81 TYR 0.009 0.001 TYR H 248 ARG 0.007 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.327 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 1.1192 time to fit residues: 56.3910 Evaluate side-chains 44 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2589 Z= 0.225 Angle : 0.587 6.188 3509 Z= 0.295 Chirality : 0.043 0.130 387 Planarity : 0.005 0.039 445 Dihedral : 10.892 175.677 345 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.93 % Favored : 95.74 % Rotamer: Outliers : 3.33 % Allowed : 15.19 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.15 (0.47), residues: 305 helix: 0.12 (0.48), residues: 110 sheet: -0.31 (1.03), residues: 22 loop : -0.10 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.014 0.002 PHE J 185 TYR 0.010 0.002 TYR J 127 ARG 0.007 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.244 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 1.0988 time to fit residues: 47.5301 Evaluate side-chains 43 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.0000 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.209 Angle : 0.572 5.870 3509 Z= 0.287 Chirality : 0.043 0.129 387 Planarity : 0.005 0.039 445 Dihedral : 10.856 175.626 345 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 3.33 % Allowed : 15.56 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.09 (0.47), residues: 305 helix: 0.20 (0.49), residues: 110 sheet: -0.26 (1.05), residues: 22 loop : -0.09 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.013 0.002 PHE J 91 TYR 0.010 0.002 TYR J 127 ARG 0.007 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.332 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 1.0823 time to fit residues: 49.0608 Evaluate side-chains 43 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Chi-restraints excluded: chain J residue 273 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2589 Z= 0.182 Angle : 0.549 5.312 3509 Z= 0.276 Chirality : 0.042 0.129 387 Planarity : 0.005 0.039 445 Dihedral : 10.774 175.303 345 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 2.22 % Allowed : 16.67 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.00 (0.48), residues: 305 helix: 0.30 (0.49), residues: 110 sheet: -0.31 (1.02), residues: 22 loop : -0.04 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.017 0.002 PHE J 185 TYR 0.010 0.001 TYR J 127 ARG 0.008 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.254 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 1.1490 time to fit residues: 51.9966 Evaluate side-chains 43 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2589 Z= 0.194 Angle : 0.567 5.351 3509 Z= 0.285 Chirality : 0.043 0.130 387 Planarity : 0.005 0.039 445 Dihedral : 10.794 175.321 345 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 2.22 % Allowed : 17.41 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.04 (0.48), residues: 305 helix: 0.27 (0.49), residues: 110 sheet: -0.29 (1.03), residues: 22 loop : -0.07 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.028 0.002 PHE J 81 TYR 0.016 0.002 TYR J 27 ARG 0.008 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.322 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 1.0942 time to fit residues: 48.4909 Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2589 Z= 0.207 Angle : 0.586 5.523 3509 Z= 0.295 Chirality : 0.043 0.132 387 Planarity : 0.005 0.041 445 Dihedral : 10.827 175.363 345 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.28 % Favored : 96.39 % Rotamer: Outliers : 1.85 % Allowed : 17.78 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.07 (0.47), residues: 305 helix: 0.20 (0.49), residues: 110 sheet: -0.25 (1.05), residues: 22 loop : -0.06 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 132 HIS 0.003 0.001 HIS J 259 PHE 0.028 0.002 PHE J 81 TYR 0.013 0.002 TYR J 127 ARG 0.009 0.001 ARG J 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 610 Ramachandran restraints generated. 305 Oldfield, 0 Emsley, 305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.286 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 42 average time/residue: 1.1194 time to fit residues: 48.3943 Evaluate side-chains 46 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS ** J 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.186198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.166920 restraints weight = 2623.925| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.25 r_work: 0.3980 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2589 Z= 0.206 Angle : 0.580 5.498 3509 Z= 0.292 Chirality : 0.043 0.132 387 Planarity : 0.005 0.041 445 Dihedral : 10.819 175.254 345 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.61 % Favored : 96.07 % Rotamer: Outliers : 1.85 % Allowed : 17.78 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.07 (0.47), residues: 305 helix: 0.20 (0.49), residues: 110 sheet: -0.31 (1.05), residues: 22 loop : -0.06 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 132 HIS 0.004 0.001 HIS J 259 PHE 0.028 0.002 PHE J 81 TYR 0.013 0.002 TYR J 127 ARG 0.009 0.001 ARG J 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.12 seconds wall clock time: 31 minutes 0.91 seconds (1860.91 seconds total)