Starting phenix.real_space_refine on Wed Jan 17 17:55:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/01_2024/8p6y_17511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/01_2024/8p6y_17511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/01_2024/8p6y_17511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/01_2024/8p6y_17511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/01_2024/8p6y_17511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6y_17511/01_2024/8p6y_17511_updated.pdb" } resolution = 1.9 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3279 2.51 5 N 869 2.21 5 O 1082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 247": "OE1" <-> "OE2" Residue "H ASP 299": "OD1" <-> "OD2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I GLU 137": "OE1" <-> "OE2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "I GLU 229": "OE1" <-> "OE2" Residue "J PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5266 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "J" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 3.59, per 1000 atoms: 0.68 Number of scatterers: 5266 At special positions: 0 Unit cell: (84.7875, 94.7625, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 3 15.00 Mg 1 11.99 O 1082 8.00 N 869 7.00 C 3279 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: 2.50 Conformation dependent library (CDL) restraints added in 949.6 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 2 sheets defined 54.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.488A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 284 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 37 Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.703A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.622A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.571A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 Processing helix chain 'I' and resid 184 through 200 removed outlier: 4.802A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 242 through 260 Processing helix chain 'I' and resid 267 through 283 Processing helix chain 'J' and resid 57 through 68 removed outlier: 4.087A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) 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 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' 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: 4.421A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 229 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: 6.743A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 218 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1669 1.36 - 1.50: 1384 1.50 - 1.64: 2120 1.64 - 1.78: 7 1.78 - 1.91: 50 Bond restraints: 5230 Sorted by residual: bond pdb=" C6 AGS J 401 " pdb=" N6 AGS J 401 " ideal model delta sigma weight residual 1.335 1.457 -0.122 1.00e-02 1.00e+04 1.48e+02 bond pdb=" C1' AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 1.459 1.319 0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 bond pdb=" O3B AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sigma weight residual 1.559 1.656 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " ideal model delta sigma weight residual 1.386 1.338 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 5225 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.55: 103 104.55 - 111.90: 2518 111.90 - 119.25: 1766 119.25 - 126.60: 2620 126.60 - 133.95: 78 Bond angle restraints: 7085 Sorted by residual: angle pdb=" N1 AGS J 401 " pdb=" C2 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 128.80 120.14 8.66 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " ideal model delta sigma weight residual 103.67 107.94 -4.27 4.26e-01 5.51e+00 1.01e+02 angle pdb=" C5 AGS J 401 " pdb=" C4 AGS J 401 " pdb=" N3 AGS J 401 " ideal model delta sigma weight residual 126.80 119.81 6.99 7.41e-01 1.82e+00 8.90e+01 angle pdb=" N7 AGS J 401 " pdb=" C8 AGS J 401 " pdb=" N9 AGS J 401 " ideal model delta sigma weight residual 114.03 108.21 5.82 6.99e-01 2.05e+00 6.93e+01 angle pdb=" C4 AGS J 401 " pdb=" C5 AGS J 401 " pdb=" N7 AGS J 401 " ideal model delta sigma weight residual 110.73 108.03 2.70 4.52e-01 4.89e+00 3.57e+01 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 2818 19.94 - 39.88: 257 39.88 - 59.81: 73 59.81 - 79.75: 11 79.75 - 99.69: 8 Dihedral angle restraints: 3167 sinusoidal: 1320 harmonic: 1847 Sorted by residual: dihedral pdb=" O1B AGS J 401 " pdb=" O3B AGS J 401 " pdb=" PB AGS J 401 " pdb=" PG AGS J 401 " ideal model delta sinusoidal sigma weight residual 68.91 168.60 -99.69 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" CB GLU I 145 " pdb=" CG GLU I 145 " pdb=" CD GLU I 145 " pdb=" OE1 GLU I 145 " ideal model delta sinusoidal sigma weight residual 0.00 90.26 -90.26 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 3164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 613 0.047 - 0.094: 131 0.094 - 0.142: 34 0.142 - 0.189: 1 0.189 - 0.236: 2 Chirality restraints: 781 Sorted by residual: chirality pdb=" C1' AGS J 401 " pdb=" C2' AGS J 401 " pdb=" N9 AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False 2.41 2.17 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C2' AGS J 401 " pdb=" C1' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" O2' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.67 -2.87 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C4' AGS J 401 " pdb=" C3' AGS J 401 " pdb=" C5' AGS J 401 " pdb=" O4' AGS J 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.63 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 778 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 66 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" CD GLU I 66 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU I 66 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU I 66 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 183 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO I 184 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO J 140 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 189 2.70 - 3.25: 5308 3.25 - 3.80: 9278 3.80 - 4.35: 12308 4.35 - 4.90: 19369 Nonbonded interactions: 46452 Sorted by model distance: nonbonded pdb="MG MG J 402 " pdb=" O HOH J 551 " model vdw 2.148 2.170 nonbonded pdb=" O ARG I 242 " pdb=" NH1 ARG I 242 " model vdw 2.203 2.520 nonbonded pdb=" O HOH J 535 " pdb=" O HOH J 561 " model vdw 2.246 2.440 nonbonded pdb=" O HOH I 402 " pdb=" O HOH I 467 " model vdw 2.255 2.440 nonbonded pdb=" O HOH J 505 " pdb=" O HOH J 539 " model vdw 2.260 2.440 ... (remaining 46447 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: 2.400 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: 0.010 Extract box with map and model: 12.570 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.340 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.005 0.140 5230 Z= 0.355 Angle : 0.600 8.826 7085 Z= 0.400 Chirality : 0.042 0.236 781 Planarity : 0.004 0.036 902 Dihedral : 17.032 99.688 1971 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.36 % Allowed : 15.34 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.99 (0.34), residues: 618 helix: 2.21 (0.29), residues: 331 sheet: -0.61 (1.27), residues: 19 loop : 0.43 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 11 HIS 0.009 0.001 HIS J 258 PHE 0.013 0.002 PHE I 110 TYR 0.016 0.001 TYR I 91 ARG 0.002 0.000 ARG I 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.629 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 1.6526 time to fit residues: 153.6615 Evaluate side-chains 87 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5230 Z= 0.165 Angle : 0.529 8.281 7085 Z= 0.267 Chirality : 0.041 0.145 781 Planarity : 0.004 0.035 902 Dihedral : 7.928 87.031 712 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.08 % Allowed : 13.90 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.94 (0.34), residues: 618 helix: 2.17 (0.29), residues: 331 sheet: -0.66 (1.27), residues: 19 loop : 0.40 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 PHE 0.013 0.002 PHE I 110 TYR 0.017 0.001 TYR I 91 ARG 0.002 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.620 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 95 average time/residue: 1.6415 time to fit residues: 161.1799 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 50 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5230 Z= 0.182 Angle : 0.546 8.197 7085 Z= 0.276 Chirality : 0.041 0.139 781 Planarity : 0.005 0.035 902 Dihedral : 7.629 80.806 709 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 13.54 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.88 (0.34), residues: 618 helix: 2.12 (0.29), residues: 331 sheet: -0.68 (1.27), residues: 19 loop : 0.38 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.002 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.671 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 95 average time/residue: 1.6453 time to fit residues: 161.3135 Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5230 Z= 0.133 Angle : 0.498 8.472 7085 Z= 0.251 Chirality : 0.040 0.134 781 Planarity : 0.004 0.033 902 Dihedral : 7.350 77.857 709 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Rotamer: Outliers : 0.72 % Allowed : 14.62 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.94 (0.34), residues: 618 helix: 2.21 (0.29), residues: 329 sheet: -0.58 (1.26), residues: 19 loop : 0.35 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 PHE 0.012 0.001 PHE I 30 TYR 0.016 0.001 TYR I 91 ARG 0.001 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.643 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 94 average time/residue: 1.5917 time to fit residues: 154.6639 Evaluate side-chains 88 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5230 Z= 0.230 Angle : 0.600 8.488 7085 Z= 0.303 Chirality : 0.043 0.153 781 Planarity : 0.005 0.036 902 Dihedral : 7.519 77.606 709 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 13.54 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.82 (0.34), residues: 618 helix: 2.04 (0.28), residues: 331 sheet: -0.74 (1.28), residues: 19 loop : 0.39 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.010 0.002 HIS J 258 PHE 0.015 0.002 PHE I 13 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.662 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 95 average time/residue: 1.5752 time to fit residues: 154.8330 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5230 Z= 0.169 Angle : 0.545 8.820 7085 Z= 0.274 Chirality : 0.041 0.140 781 Planarity : 0.004 0.036 902 Dihedral : 7.403 77.434 709 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 14.08 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.88 (0.34), residues: 618 helix: 2.11 (0.29), residues: 331 sheet: -0.75 (1.27), residues: 19 loop : 0.41 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.009 0.001 HIS J 258 PHE 0.014 0.002 PHE I 30 TYR 0.017 0.001 TYR I 91 ARG 0.002 0.000 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.664 Fit side-chains REVERT: I 18 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7942 (tt0) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 1.7067 time to fit residues: 165.5569 Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5230 Z= 0.254 Angle : 0.635 9.048 7085 Z= 0.320 Chirality : 0.044 0.158 781 Planarity : 0.005 0.037 902 Dihedral : 7.572 77.542 709 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.71 (0.34), residues: 618 helix: 1.94 (0.28), residues: 331 sheet: -1.02 (1.22), residues: 19 loop : 0.39 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.010 0.002 HIS J 258 PHE 0.017 0.002 PHE I 71 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.692 Fit side-chains REVERT: I 18 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7934 (tt0) outliers start: 9 outliers final: 7 residues processed: 93 average time/residue: 1.7099 time to fit residues: 164.1952 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 124 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5230 Z= 0.386 Angle : 0.763 9.761 7085 Z= 0.387 Chirality : 0.049 0.198 781 Planarity : 0.006 0.045 902 Dihedral : 7.808 78.750 709 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.81 % Allowed : 13.90 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.34), residues: 618 helix: 1.70 (0.27), residues: 331 sheet: -1.36 (1.09), residues: 19 loop : 0.36 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP J 132 HIS 0.011 0.003 HIS J 131 PHE 0.022 0.003 PHE I 71 TYR 0.022 0.003 TYR I 91 ARG 0.005 0.001 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.645 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 1.5564 time to fit residues: 148.1072 Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 55 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5230 Z= 0.186 Angle : 0.584 10.246 7085 Z= 0.294 Chirality : 0.042 0.143 781 Planarity : 0.005 0.039 902 Dihedral : 7.535 78.844 709 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.72 % Allowed : 15.34 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.78 (0.34), residues: 618 helix: 2.01 (0.28), residues: 331 sheet: -0.68 (1.01), residues: 25 loop : 0.39 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.010 0.001 HIS J 258 PHE 0.015 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.002 0.000 ARG I 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.635 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 93 average time/residue: 1.6006 time to fit residues: 153.8423 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5230 Z= 0.253 Angle : 0.649 9.669 7085 Z= 0.328 Chirality : 0.044 0.156 781 Planarity : 0.005 0.039 902 Dihedral : 7.615 77.871 709 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 14.80 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.71 (0.34), residues: 618 helix: 1.93 (0.28), residues: 331 sheet: -1.11 (1.18), residues: 19 loop : 0.41 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.010 0.002 HIS J 258 PHE 0.018 0.002 PHE I 71 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.000 ARG I 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.667 Fit side-chains REVERT: I 18 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7910 (tt0) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 1.6065 time to fit residues: 154.3903 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 166 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** J 83 HIS ** 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 = 0.3864 r_free = 0.3864 target = 0.157740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133545 restraints weight = 4461.366| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 0.82 r_work: 0.3408 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5230 Z= 0.192 Angle : 0.589 9.575 7085 Z= 0.297 Chirality : 0.042 0.144 781 Planarity : 0.005 0.039 902 Dihedral : 7.498 77.846 709 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.08 % Allowed : 14.98 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.34), residues: 618 helix: 2.02 (0.28), residues: 329 sheet: -0.64 (1.03), residues: 25 loop : 0.31 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.010 0.001 HIS J 258 PHE 0.016 0.002 PHE I 71 TYR 0.017 0.002 TYR I 91 ARG 0.002 0.000 ARG I 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2998.78 seconds wall clock time: 53 minutes 34.60 seconds (3214.60 seconds total)