Starting phenix.real_space_refine on Sun Mar 10 21:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/03_2024/8p6v_17508_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/03_2024/8p6v_17508.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/8p6v_17508/03_2024/8p6v_17508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/03_2024/8p6v_17508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/03_2024/8p6v_17508_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6v_17508/03_2024/8p6v_17508_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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3291 2.51 5 N 870 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 17": "OE1" <-> "OE2" Residue "I ASP 250": "OD1" <-> "OD2" Residue "I GLU 268": "OE1" <-> "OE2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "J ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5243 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'I74': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 3.56, per 1000 atoms: 0.68 Number of scatterers: 5243 At special positions: 0 Unit cell: (84.7875, 94.05, 69.1125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1051 8.00 N 870 7.00 C 3291 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: 2.18 Conformation dependent library (CDL) restraints added in 872.0 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 54.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.122A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 269 " --> pdb=" O LEU H 266 " (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 70 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.827A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 4.034A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.570A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.402A 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: 4.920A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA I 191 " --> pdb=" O ARG I 188 " (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 234 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 261 Processing helix chain 'I' and resid 267 through 283 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 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: 4.123A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.818A 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 291 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: 6.797A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 25 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 220 hydrogen bonds defined for protein. 576 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: 1.40 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1637 1.34 - 1.46: 969 1.46 - 1.58: 2572 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5229 Sorted by residual: bond pdb=" C3 I74 J 401 " pdb=" N10 I74 J 401 " ideal model delta sigma weight residual 1.335 1.489 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C26 I74 J 401 " pdb=" C8 I74 J 401 " ideal model delta sigma weight residual 1.497 1.602 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 I74 J 401 " pdb=" N18 I74 J 401 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C41 I74 J 401 " pdb=" C46 I74 J 401 " ideal model delta sigma weight residual 1.532 1.456 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C40 I74 J 401 " pdb=" C41 I74 J 401 " ideal model delta sigma weight residual 1.524 1.592 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 5224 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.68: 139 105.68 - 112.74: 2729 112.74 - 119.81: 1750 119.81 - 126.87: 2388 126.87 - 133.93: 71 Bond angle restraints: 7077 Sorted by residual: angle pdb=" CA LYS I 260 " pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.68e+00 angle pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " pdb=" CD LYS J 293 " ideal model delta sigma weight residual 111.30 118.04 -6.74 2.30e+00 1.89e-01 8.59e+00 angle pdb=" CA GLU I 268 " pdb=" CB GLU I 268 " pdb=" CG GLU I 268 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.45 4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " pdb=" CD LYS I 260 " ideal model delta sigma weight residual 111.30 116.85 -5.55 2.30e+00 1.89e-01 5.82e+00 ... (remaining 7072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 2791 17.41 - 34.83: 270 34.83 - 52.24: 73 52.24 - 69.65: 17 69.65 - 87.06: 13 Dihedral angle restraints: 3164 sinusoidal: 1317 harmonic: 1847 Sorted by residual: dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N ARG J 176 " pdb=" CA ARG J 176 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG J 176 " pdb=" CD ARG J 176 " pdb=" NE ARG J 176 " pdb=" CZ ARG J 176 " ideal model delta sinusoidal sigma weight residual 180.00 136.01 43.99 2 1.50e+01 4.44e-03 1.03e+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 180.00 164.41 15.59 0 5.00e+00 4.00e-02 9.72e+00 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 445 0.028 - 0.057: 210 0.057 - 0.085: 75 0.085 - 0.114: 39 0.114 - 0.142: 8 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-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 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL H 260 " pdb=" N VAL H 260 " pdb=" C VAL H 260 " pdb=" CB VAL H 260 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 14 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C LYS J 14 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS J 14 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU J 15 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO I 163 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 201 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C CYS J 201 " -0.021 2.00e-02 2.50e+03 pdb=" O CYS J 201 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE J 202 " 0.007 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 846 2.76 - 3.29: 5347 3.29 - 3.83: 9809 3.83 - 4.36: 11859 4.36 - 4.90: 19012 Nonbonded interactions: 46873 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.221 2.440 nonbonded pdb=" O LEU I 236 " pdb=" O HOH I 401 " model vdw 2.225 2.440 nonbonded pdb=" O MET J 189 " pdb=" O HOH J 501 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR I 178 " pdb=" OG SER I 230 " model vdw 2.238 2.440 nonbonded pdb=" O HOH J 567 " pdb=" O HOH J 571 " model vdw 2.243 2.440 ... (remaining 46868 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.460 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.000 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:14.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 0.154 5229 Z= 0.289 Angle : 0.616 8.587 7077 Z= 0.309 Chirality : 0.041 0.142 777 Planarity : 0.004 0.031 903 Dihedral : 16.303 87.063 1968 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 13.90 % 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: 1.53 (0.34), residues: 618 helix: 1.80 (0.28), residues: 337 sheet: 0.43 (1.28), residues: 20 loop : 0.10 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.015 0.002 PHE I 110 TYR 0.015 0.002 TYR I 91 ARG 0.007 0.000 ARG H 268 *********************** 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 93 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.644 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 1.4016 time to fit residues: 133.8418 Evaluate side-chains 89 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 249 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.0020 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 259 HIS I 142 GLN J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5229 Z= 0.151 Angle : 0.507 7.934 7077 Z= 0.261 Chirality : 0.040 0.133 777 Planarity : 0.004 0.029 903 Dihedral : 8.237 89.056 717 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.61 % Allowed : 12.64 % Favored : 83.75 % 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: 1.72 (0.35), residues: 618 helix: 1.94 (0.28), residues: 337 sheet: 0.83 (1.41), residues: 20 loop : 0.19 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.013 0.001 PHE I 110 TYR 0.014 0.002 TYR I 91 ARG 0.005 0.000 ARG H 268 *********************** 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 106 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.573 Fit side-chains REVERT: J 14 LYS cc_start: 0.6222 (tppt) cc_final: 0.5887 (tppt) REVERT: J 169 TYR cc_start: 0.5996 (OUTLIER) cc_final: 0.5786 (m-80) outliers start: 20 outliers final: 6 residues processed: 100 average time/residue: 1.4044 time to fit residues: 145.6145 Evaluate side-chains 90 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5229 Z= 0.233 Angle : 0.582 8.475 7077 Z= 0.299 Chirality : 0.042 0.139 777 Planarity : 0.005 0.030 903 Dihedral : 7.623 88.104 708 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.53 % Allowed : 14.08 % Favored : 83.39 % 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: 1.38 (0.34), residues: 618 helix: 1.68 (0.28), residues: 336 sheet: 0.20 (1.23), residues: 20 loop : 0.07 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.005 0.002 HIS J 131 PHE 0.013 0.002 PHE I 110 TYR 0.018 0.002 TYR I 91 ARG 0.005 0.001 ARG H 268 *********************** 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 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.624 Fit side-chains REVERT: J 147 GLU cc_start: 0.6850 (pm20) cc_final: 0.6640 (pm20) outliers start: 14 outliers final: 6 residues processed: 95 average time/residue: 1.4986 time to fit residues: 147.3982 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5229 Z= 0.228 Angle : 0.584 8.647 7077 Z= 0.300 Chirality : 0.042 0.144 777 Planarity : 0.005 0.031 903 Dihedral : 7.628 88.679 708 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 4.15 % Allowed : 12.45 % Favored : 83.39 % 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: 1.26 (0.34), residues: 618 helix: 1.59 (0.28), residues: 336 sheet: -0.02 (1.15), residues: 20 loop : 0.00 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.006 0.002 HIS H 259 PHE 0.013 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG H 268 *********************** 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 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.654 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 100 average time/residue: 1.4732 time to fit residues: 152.5835 Evaluate side-chains 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5229 Z= 0.275 Angle : 0.629 8.734 7077 Z= 0.323 Chirality : 0.044 0.144 777 Planarity : 0.005 0.032 903 Dihedral : 7.680 88.633 708 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 4.15 % Allowed : 13.00 % Favored : 82.85 % 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: 1.08 (0.34), residues: 618 helix: 1.44 (0.28), residues: 336 sheet: -0.33 (1.12), residues: 20 loop : -0.06 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 132 HIS 0.006 0.002 HIS H 259 PHE 0.014 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.004 0.001 ARG H 268 *********************** 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 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.609 Fit side-chains REVERT: J 62 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: J 147 GLU cc_start: 0.6912 (pm20) cc_final: 0.6668 (mp0) outliers start: 23 outliers final: 12 residues processed: 102 average time/residue: 1.4377 time to fit residues: 151.9550 Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 258 HIS J 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5229 Z= 0.183 Angle : 0.539 7.758 7077 Z= 0.275 Chirality : 0.041 0.142 777 Planarity : 0.004 0.030 903 Dihedral : 7.589 89.428 708 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 13.90 % Favored : 83.03 % 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: 1.35 (0.34), residues: 618 helix: 1.71 (0.28), residues: 336 sheet: 0.03 (1.15), residues: 20 loop : -0.03 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.014 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.004 0.000 ARG I 279 *********************** 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 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.655 Fit side-chains REVERT: J 147 GLU cc_start: 0.6799 (pm20) cc_final: 0.6590 (mp0) outliers start: 17 outliers final: 11 residues processed: 99 average time/residue: 1.4816 time to fit residues: 152.0985 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS J 258 HIS J 259 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5229 Z= 0.164 Angle : 0.521 7.439 7077 Z= 0.266 Chirality : 0.040 0.140 777 Planarity : 0.004 0.029 903 Dihedral : 7.556 89.702 708 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.71 % Allowed : 14.08 % Favored : 83.21 % 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: 1.56 (0.34), residues: 618 helix: 1.88 (0.29), residues: 330 sheet: 0.33 (1.24), residues: 20 loop : 0.10 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.013 0.002 PHE I 110 TYR 0.015 0.002 TYR I 91 ARG 0.004 0.000 ARG I 279 *********************** 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 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.609 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 1.4674 time to fit residues: 145.9092 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 258 HIS J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5229 Z= 0.171 Angle : 0.527 7.598 7077 Z= 0.269 Chirality : 0.040 0.140 777 Planarity : 0.004 0.029 903 Dihedral : 7.557 90.000 708 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.07 % Allowed : 14.26 % Favored : 82.67 % 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: 1.57 (0.34), residues: 618 helix: 1.86 (0.29), residues: 330 sheet: 0.37 (1.22), residues: 20 loop : 0.13 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 PHE 0.013 0.001 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.004 0.000 ARG I 279 *********************** 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 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.650 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 1.4728 time to fit residues: 146.4009 Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.0170 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 258 HIS J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5229 Z= 0.145 Angle : 0.518 7.830 7077 Z= 0.265 Chirality : 0.039 0.137 777 Planarity : 0.004 0.029 903 Dihedral : 7.473 88.596 708 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 2.71 % Allowed : 14.62 % Favored : 82.67 % 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: 1.75 (0.35), residues: 618 helix: 2.00 (0.29), residues: 331 sheet: 0.71 (1.27), residues: 20 loop : 0.21 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.013 0.001 PHE I 110 TYR 0.015 0.001 TYR I 60 ARG 0.007 0.000 ARG I 279 *********************** 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 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.627 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 1.4141 time to fit residues: 143.6364 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL 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: 0.1980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.0040 chunk 15 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS J 258 HIS J 259 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5229 Z= 0.154 Angle : 0.515 8.188 7077 Z= 0.261 Chirality : 0.039 0.136 777 Planarity : 0.004 0.029 903 Dihedral : 7.473 88.811 708 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 14.80 % Favored : 82.67 % 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: 1.75 (0.34), residues: 618 helix: 1.92 (0.29), residues: 332 sheet: 0.83 (1.30), residues: 20 loop : 0.30 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 PHE 0.012 0.001 PHE J 252 TYR 0.014 0.002 TYR I 60 ARG 0.008 0.000 ARG I 279 ********************** 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 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.651 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 1.4227 time to fit residues: 137.1394 Evaluate side-chains 91 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 259 HIS I 142 GLN J 258 HIS J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.176003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153334 restraints weight = 4744.946| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 0.97 r_work: 0.3750 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5229 Z= 0.227 Angle : 0.601 10.130 7077 Z= 0.306 Chirality : 0.042 0.138 777 Planarity : 0.005 0.030 903 Dihedral : 7.608 89.778 708 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 15.16 % Favored : 82.31 % 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: 1.46 (0.34), residues: 618 helix: 1.70 (0.29), residues: 330 sheet: 0.41 (1.17), residues: 20 loop : 0.19 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.007 0.002 HIS H 259 PHE 0.012 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.008 0.001 ARG I 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3003.86 seconds wall clock time: 53 minutes 30.43 seconds (3210.43 seconds total)