Starting phenix.real_space_refine on Fri Mar 15 10:25:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk9_25177/03_2024/7sk9_25177_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk9_25177/03_2024/7sk9_25177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk9_25177/03_2024/7sk9_25177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk9_25177/03_2024/7sk9_25177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk9_25177/03_2024/7sk9_25177_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk9_25177/03_2024/7sk9_25177_trim_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.056 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 3711 2.51 5 N 918 2.21 5 O 1042 1.98 5 H 5561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 11261 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 4660 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 282, 4660 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 bond proxies already assigned to first conformer: 4712 Chain: "F" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3280 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3213 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 200} Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'CLR': 2, 'GJ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS A 291 " occ=0.50 ... (29 atoms not shown) pdb=" HE2BHIS A 291 " occ=0.50 Time building chain proxies: 7.56, per 1000 atoms: 0.67 Number of scatterers: 11261 At special positions: 0 Unit cell: (60.48, 64.8, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 1042 8.00 N 918 7.00 C 3711 6.00 H 5561 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.04 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.16 Conformation dependent library (CDL) restraints added in 1.8 seconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 8 sheets defined 34.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 41 through 75 removed outlier: 4.211A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 105 Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.760A pdb=" N SER A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 154 through 182 Proline residue: A 178 - end of helix removed outlier: 3.730A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 222 through 241 Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.890A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 248' Processing helix chain 'A' and resid 254 through 279 removed outlier: 4.018A pdb=" N PHE A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 287 through 309 removed outlier: 3.612A pdb=" N LEU A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 306 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 320 through 328 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'E' and resid 125 through 128 Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 184 through 189 Processing sheet with id= A, first strand: chain 'F' and resid 20 through 26 Processing sheet with id= B, first strand: chain 'F' and resid 95 through 102 removed outlier: 3.895A pdb=" N SER F 36 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA F 43 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU F 48 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.095A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.741A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN F 216 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR F 211 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 6 through 8 Processing sheet with id= F, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.651A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.637A pdb=" N ALA E 131 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN E 139 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 146 through 149 246 hydrogen bonds defined for protein. 704 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: 3.63 Time building geometry restraints manager: 9.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5552 1.03 - 1.23: 29 1.23 - 1.42: 2489 1.42 - 1.62: 3314 1.62 - 1.82: 39 Bond restraints: 11423 Sorted by residual: bond pdb=" C14 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.416 1.492 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.495 1.558 -0.063 2.00e-02 2.50e+03 9.80e+00 bond pdb=" C32 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.457 1.517 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.446 1.505 -0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" C11 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.497 1.551 -0.054 2.00e-02 2.50e+03 7.32e+00 ... (remaining 11418 not shown) Histogram of bond angle deviations from ideal: 89.74 - 98.59: 2 98.59 - 107.44: 456 107.44 - 116.30: 14173 116.30 - 125.15: 5569 125.15 - 134.00: 357 Bond angle restraints: 20557 Sorted by residual: angle pdb=" C22 CLR A 403 " pdb=" C23 CLR A 403 " pdb=" C24 CLR A 403 " ideal model delta sigma weight residual 111.95 104.13 7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" C22 CLR A 402 " pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " ideal model delta sigma weight residual 111.95 104.37 7.58 3.00e+00 1.11e-01 6.39e+00 angle pdb=" C33 GJ9 A 401 " pdb=" C32 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 112.14 119.71 -7.57 3.00e+00 1.11e-01 6.37e+00 angle pdb=" C08 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 108.48 116.01 -7.53 3.00e+00 1.11e-01 6.29e+00 angle pdb=" C06 GJ9 A 401 " pdb=" N05 GJ9 A 401 " pdb=" C37 GJ9 A 401 " ideal model delta sigma weight residual 121.17 114.07 7.10 3.00e+00 1.11e-01 5.61e+00 ... (remaining 20552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 5377 29.04 - 58.08: 206 58.08 - 87.12: 5 87.12 - 116.16: 6 116.16 - 145.19: 5 Dihedral angle restraints: 5599 sinusoidal: 3008 harmonic: 2591 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 178.86 -85.86 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" N10 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sinusoidal sigma weight residual -73.26 71.93 -145.19 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C11 GJ9 A 401 " pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " pdb=" C14 GJ9 A 401 " ideal model delta sinusoidal sigma weight residual 193.62 60.62 133.00 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 846 0.075 - 0.151: 67 0.151 - 0.226: 1 0.226 - 0.301: 2 0.301 - 0.376: 6 Chirality restraints: 922 Sorted by residual: chirality pdb=" C17 CLR A 403 " pdb=" C13 CLR A 403 " pdb=" C16 CLR A 403 " pdb=" C20 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" N10 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C34 GJ9 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.59 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.87 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 919 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 209 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C LEU A 209 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 209 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 210 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 225 " 0.011 2.00e-02 2.50e+03 6.79e-03 1.39e+00 pdb=" CG PHE A 225 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 225 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 225 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 225 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 225 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 225 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 225 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO F 166 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " -0.015 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1443 2.25 - 2.84: 24653 2.84 - 3.42: 27479 3.42 - 4.01: 38307 4.01 - 4.60: 58098 Nonbonded interactions: 149980 Sorted by model distance: nonbonded pdb=" O GLN A 106 " pdb=" H GLN A 109 " model vdw 1.662 1.850 nonbonded pdb=" O HIS E 190 " pdb=" HE ARG E 212 " model vdw 1.706 1.850 nonbonded pdb=" O ASP E 83 " pdb=" HH TYR E 87 " model vdw 1.731 1.850 nonbonded pdb=" O THR A 147 " pdb=" HG SER F 57 " model vdw 1.744 1.850 nonbonded pdb=" H ILE F 32 " pdb=" OD1 ASN F 80 " model vdw 1.745 1.850 ... (remaining 149975 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.180 Extract box with map and model: 6.380 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 41.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 0.076 5862 Z= 0.304 Angle : 0.620 7.825 8006 Z= 0.288 Chirality : 0.050 0.376 922 Planarity : 0.003 0.029 966 Dihedral : 15.645 145.195 2177 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.15 (0.35), residues: 707 helix: 2.71 (0.36), residues: 222 sheet: 0.15 (0.41), residues: 198 loop : -0.29 (0.41), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 171 HIS 0.004 0.001 HIS A 121 PHE 0.020 0.001 PHE A 225 TYR 0.018 0.001 TYR A 181 ARG 0.002 0.000 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.985 Fit side-chains REVERT: E 25 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7382 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3273 time to fit residues: 39.4852 Evaluate side-chains 69 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5862 Z= 0.193 Angle : 0.505 5.904 8006 Z= 0.255 Chirality : 0.039 0.142 922 Planarity : 0.003 0.031 966 Dihedral : 12.218 142.937 946 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.47 % Allowed : 6.46 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.35), residues: 707 helix: 2.78 (0.35), residues: 229 sheet: 0.06 (0.39), residues: 205 loop : -0.24 (0.42), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.015 0.001 PHE A 225 TYR 0.014 0.001 TYR A 181 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.973 Fit side-chains REVERT: E 25 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7342 (ttm-80) outliers start: 3 outliers final: 2 residues processed: 74 average time/residue: 0.3597 time to fit residues: 36.0886 Evaluate side-chains 73 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5862 Z= 0.214 Angle : 0.503 7.514 8006 Z= 0.255 Chirality : 0.039 0.141 922 Planarity : 0.003 0.031 966 Dihedral : 9.109 129.326 946 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.79 % Allowed : 7.09 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.18 (0.35), residues: 707 helix: 2.79 (0.35), residues: 229 sheet: 0.04 (0.39), residues: 205 loop : -0.32 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.017 0.001 PHE A 225 TYR 0.012 0.001 TYR F 162 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.022 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.3450 time to fit residues: 33.0850 Evaluate side-chains 68 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 43 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5862 Z= 0.137 Angle : 0.475 6.330 8006 Z= 0.236 Chirality : 0.039 0.130 922 Planarity : 0.003 0.029 966 Dihedral : 5.927 57.857 946 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.79 % Allowed : 6.93 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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 (0.35), residues: 707 helix: 2.99 (0.35), residues: 229 sheet: -0.12 (0.38), residues: 219 loop : -0.03 (0.43), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 171 HIS 0.002 0.001 HIS A 298 PHE 0.017 0.001 PHE A 225 TYR 0.016 0.001 TYR A 181 ARG 0.001 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: E 25 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7451 (ttm-80) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.3582 time to fit residues: 35.2599 Evaluate side-chains 70 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5862 Z= 0.207 Angle : 0.479 4.921 8006 Z= 0.246 Chirality : 0.039 0.130 922 Planarity : 0.003 0.031 966 Dihedral : 5.517 58.367 946 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.26 % Allowed : 7.72 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.27 (0.35), residues: 707 helix: 2.91 (0.35), residues: 229 sheet: 0.08 (0.40), residues: 205 loop : -0.30 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 80 PHE 0.018 0.001 PHE A 225 TYR 0.013 0.001 TYR A 181 ARG 0.001 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.744 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 0.3713 time to fit residues: 34.9063 Evaluate side-chains 70 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5862 Z= 0.154 Angle : 0.461 4.560 8006 Z= 0.235 Chirality : 0.038 0.129 922 Planarity : 0.003 0.031 966 Dihedral : 5.079 57.219 946 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.10 % Allowed : 8.35 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.29 (0.35), residues: 707 helix: 3.00 (0.35), residues: 229 sheet: -0.16 (0.38), residues: 219 loop : -0.11 (0.43), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 171 HIS 0.002 0.001 HIS A 298 PHE 0.017 0.001 PHE A 225 TYR 0.009 0.001 TYR F 162 ARG 0.002 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: E 25 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7446 (ttm-80) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.3224 time to fit residues: 31.2398 Evaluate side-chains 71 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5862 Z= 0.252 Angle : 0.506 4.665 8006 Z= 0.262 Chirality : 0.039 0.134 922 Planarity : 0.003 0.033 966 Dihedral : 5.437 63.821 946 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.10 % Allowed : 8.82 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.18 (0.35), residues: 707 helix: 2.79 (0.35), residues: 229 sheet: 0.01 (0.40), residues: 204 loop : -0.29 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.004 0.001 HIS A 80 PHE 0.018 0.001 PHE A 225 TYR 0.018 0.001 TYR A 181 ARG 0.001 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.912 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.3613 time to fit residues: 32.9258 Evaluate side-chains 69 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5862 Z= 0.171 Angle : 0.475 4.458 8006 Z= 0.243 Chirality : 0.039 0.131 922 Planarity : 0.003 0.032 966 Dihedral : 5.216 60.689 946 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.94 % Allowed : 9.13 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.35), residues: 707 helix: 2.91 (0.35), residues: 229 sheet: -0.06 (0.39), residues: 211 loop : -0.24 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 171 HIS 0.002 0.001 HIS A 121 PHE 0.018 0.001 PHE A 225 TYR 0.017 0.001 TYR A 181 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.896 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 0.3098 time to fit residues: 29.0998 Evaluate side-chains 69 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5862 Z= 0.245 Angle : 0.505 4.619 8006 Z= 0.262 Chirality : 0.039 0.133 922 Planarity : 0.003 0.033 966 Dihedral : 5.439 64.344 946 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.94 % Allowed : 9.29 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.07 (0.34), residues: 707 helix: 2.75 (0.34), residues: 229 sheet: -0.06 (0.39), residues: 209 loop : -0.40 (0.42), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 80 PHE 0.019 0.001 PHE A 225 TYR 0.019 0.001 TYR A 181 ARG 0.002 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.020 Fit side-chains REVERT: E 25 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7380 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.3744 time to fit residues: 33.2470 Evaluate side-chains 67 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5862 Z= 0.158 Angle : 0.474 4.425 8006 Z= 0.242 Chirality : 0.039 0.132 922 Planarity : 0.003 0.031 966 Dihedral : 5.170 60.132 946 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.94 % Allowed : 9.29 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.35), residues: 707 helix: 2.93 (0.35), residues: 229 sheet: -0.06 (0.38), residues: 211 loop : -0.25 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 171 HIS 0.002 0.001 HIS A 121 PHE 0.018 0.001 PHE A 225 TYR 0.017 0.001 TYR A 181 ARG 0.001 0.000 ARG E 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: E 25 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7505 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.4136 time to fit residues: 39.6482 Evaluate side-chains 69 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094686 restraints weight = 37856.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099191 restraints weight = 18031.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102187 restraints weight = 10928.215| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5862 Z= 0.195 Angle : 0.482 4.543 8006 Z= 0.248 Chirality : 0.039 0.130 922 Planarity : 0.003 0.032 966 Dihedral : 5.216 60.984 946 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.94 % Allowed : 9.45 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.17 (0.35), residues: 707 helix: 2.87 (0.35), residues: 229 sheet: -0.08 (0.39), residues: 211 loop : -0.30 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.019 0.001 PHE A 225 TYR 0.017 0.001 TYR A 181 ARG 0.001 0.000 ARG A 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.35 seconds wall clock time: 54 minutes 2.25 seconds (3242.25 seconds total)