Starting phenix.real_space_refine on Tue Feb 11 10:28:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6x_17510/02_2025/8p6x_17510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6x_17510/02_2025/8p6x_17510.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/cci-nas-00/data/ceres_data/8p6x_17510/02_2025/8p6x_17510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6x_17510/02_2025/8p6x_17510.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6x_17510/02_2025/8p6x_17510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6x_17510/02_2025/8p6x_17510.cif" } 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 3315 2.51 5 N 875 2.21 5 O 1063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5284 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: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2291 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 268} Chain breaks: 2 Chain: "J" Number of atoms: 56 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 28 Unusual residues: {'NS9': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 28 Unusual residues: {'NS9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C11ANS9 J 401 " occ=0.51 ... (54 atoms not shown) pdb=" O25BNS9 J 401 " occ=0.49 Time building chain proxies: 4.46, per 1000 atoms: 0.84 Number of scatterers: 5284 At special positions: 0 Unit cell: (84.7875, 94.05, 67.6875, 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 1063 8.00 N 875 7.00 C 3315 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 581.7 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.819A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.883A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.685A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.674A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 removed outlier: 3.569A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.627A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.044A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 284 removed outlier: 3.582A pdb=" N VAL I 272 " --> pdb=" O GLU I 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.901A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 155 through 159 removed outlier: 4.415A pdb=" N LEU J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.518A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 removed outlier: 3.677A pdb=" N LEU J 243 " --> pdb=" O MET J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 17 through 20 removed outlier: 6.436A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 272 hydrogen bonds defined for protein. 759 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: 1.47 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1648 1.34 - 1.46: 1220 1.46 - 1.58: 2348 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 5265 Sorted by residual: bond pdb=" C3 BNS9 J 401 " pdb=" N10BNS9 J 401 " ideal model delta sigma weight residual 1.335 1.445 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C3 ANS9 J 401 " pdb=" N10ANS9 J 401 " ideal model delta sigma weight residual 1.335 1.444 -0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C5 BNS9 J 401 " pdb=" N18BNS9 J 401 " ideal model delta sigma weight residual 1.355 1.450 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C5 ANS9 J 401 " pdb=" N18ANS9 J 401 " ideal model delta sigma weight residual 1.355 1.448 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C7 ANS9 J 401 " pdb=" N2 ANS9 J 401 " ideal model delta sigma weight residual 1.376 1.300 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 5260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 6978 1.86 - 3.72: 115 3.72 - 5.58: 26 5.58 - 7.43: 5 7.43 - 9.29: 2 Bond angle restraints: 7126 Sorted by residual: angle pdb=" CB MET I 237 " pdb=" CG MET I 237 " pdb=" SD MET I 237 " ideal model delta sigma weight residual 112.70 121.99 -9.29 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CA GLU I 229 " pdb=" CB GLU I 229 " pdb=" CG GLU I 229 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.52 4.38 1.80e+00 3.09e-01 5.92e+00 angle pdb=" CA LEU J 219 " pdb=" CB LEU J 219 " pdb=" CG LEU J 219 " ideal model delta sigma weight residual 116.30 124.77 -8.47 3.50e+00 8.16e-02 5.85e+00 angle pdb=" CA ARG I 28 " pdb=" CB ARG I 28 " pdb=" CG ARG I 28 " ideal model delta sigma weight residual 114.10 118.90 -4.80 2.00e+00 2.50e-01 5.75e+00 ... (remaining 7121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 2759 17.49 - 34.98: 325 34.98 - 52.46: 61 52.46 - 69.95: 25 69.95 - 87.44: 8 Dihedral angle restraints: 3178 sinusoidal: 1328 harmonic: 1850 Sorted by residual: 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 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU J 95 " pdb=" CG GLU J 95 " pdb=" CD GLU J 95 " pdb=" OE1 GLU J 95 " ideal model delta sinusoidal sigma weight residual 0.00 87.44 -87.44 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " pdb=" CZ ARG I 279 " ideal model delta sinusoidal sigma weight residual 90.00 131.87 -41.87 2 1.50e+01 4.44e-03 9.50e+00 ... (remaining 3175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 536 0.037 - 0.074: 171 0.074 - 0.111: 59 0.111 - 0.149: 12 0.149 - 0.186: 3 Chirality restraints: 781 Sorted by residual: chirality pdb=" C19BNS9 J 401 " pdb=" C20BNS9 J 401 " pdb=" C23BNS9 J 401 " pdb=" N18BNS9 J 401 " both_signs ideal model delta sigma weight residual False 2.42 2.60 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" C19ANS9 J 401 " pdb=" C20ANS9 J 401 " pdb=" C23ANS9 J 401 " pdb=" N18ANS9 J 401 " both_signs ideal model delta sigma weight residual False 2.42 2.60 -0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" C20ANS9 J 401 " pdb=" C19ANS9 J 401 " pdb=" C21ANS9 J 401 " pdb=" O25ANS9 J 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.52 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 778 not shown) Planarity restraints: 906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.13e+00 pdb=" N PRO I 166 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 198 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ALA J 198 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA J 198 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL J 199 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 199 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C VAL J 199 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL J 199 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY J 200 " 0.007 2.00e-02 2.50e+03 ... (remaining 903 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 675 2.75 - 3.29: 5469 3.29 - 3.82: 9989 3.82 - 4.36: 11922 4.36 - 4.90: 19406 Nonbonded interactions: 47461 Sorted by model distance: nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.211 3.040 nonbonded pdb=" O HOH J 501 " pdb=" O HOH J 550 " model vdw 2.230 3.040 nonbonded pdb=" O LEU I 236 " pdb=" O HOH I 401 " model vdw 2.244 3.040 nonbonded pdb=" O HOH J 555 " pdb=" O HOH J 560 " model vdw 2.258 3.040 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 402 " model vdw 2.262 3.040 ... (remaining 47456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.49 max=1.00 mean=0.99 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: 4.540 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.800 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 0.110 5265 Z= 0.304 Angle : 0.628 9.294 7126 Z= 0.295 Chirality : 0.042 0.186 781 Planarity : 0.004 0.036 906 Dihedral : 16.385 87.437 1980 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 0.72 % Allowed : 14.23 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.34), residues: 619 helix: 1.92 (0.28), residues: 336 sheet: 0.02 (1.52), residues: 18 loop : 0.29 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 258 PHE 0.016 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.006 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.632 Fit side-chains REVERT: H 259 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6609 (t-90) outliers start: 4 outliers final: 1 residues processed: 100 average time/residue: 1.5138 time to fit residues: 156.8290 Evaluate side-chains 92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 236 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 48 optimal weight: 0.0370 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 258 HIS J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.190660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159553 restraints weight = 20468.576| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.25 r_work: 0.3805 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5265 Z= 0.139 Angle : 0.511 6.835 7126 Z= 0.260 Chirality : 0.039 0.125 781 Planarity : 0.004 0.038 906 Dihedral : 7.212 64.496 720 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 13.51 % Favored : 85.05 % 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: 2.15 (0.34), residues: 619 helix: 2.42 (0.28), residues: 334 sheet: -0.84 (1.24), residues: 18 loop : 0.38 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 132 HIS 0.007 0.001 HIS J 259 PHE 0.014 0.001 PHE I 110 TYR 0.016 0.001 TYR I 91 ARG 0.004 0.000 ARG J 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.621 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 105 average time/residue: 1.3770 time to fit residues: 150.1534 Evaluate side-chains 91 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.186992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155666 restraints weight = 17195.070| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.24 r_work: 0.3759 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5265 Z= 0.226 Angle : 0.590 7.282 7126 Z= 0.299 Chirality : 0.042 0.137 781 Planarity : 0.005 0.035 906 Dihedral : 7.346 68.439 716 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 13.69 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.33), residues: 619 helix: 2.09 (0.28), residues: 334 sheet: -1.30 (1.22), residues: 11 loop : 0.23 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.021 0.002 TYR I 2 ARG 0.003 0.000 ARG J 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.613 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 1.4693 time to fit residues: 151.1262 Evaluate side-chains 92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 HIS I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.185397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153264 restraints weight = 21109.262| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.33 r_work: 0.3718 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5265 Z= 0.296 Angle : 0.655 7.092 7126 Z= 0.333 Chirality : 0.045 0.145 781 Planarity : 0.005 0.036 906 Dihedral : 7.562 69.666 716 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 12.97 % Favored : 85.05 % 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 (0.33), residues: 619 helix: 1.69 (0.28), residues: 334 sheet: -1.13 (1.03), residues: 11 loop : 0.06 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.024 0.003 TYR I 2 ARG 0.004 0.001 ARG I 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.565 Fit side-chains REVERT: I 18 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6801 (tp40) outliers start: 11 outliers final: 4 residues processed: 102 average time/residue: 1.4546 time to fit residues: 154.0087 Evaluate side-chains 97 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.187728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156313 restraints weight = 21372.511| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.28 r_work: 0.3765 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5265 Z= 0.173 Angle : 0.551 7.569 7126 Z= 0.282 Chirality : 0.041 0.133 781 Planarity : 0.004 0.037 906 Dihedral : 7.258 68.059 716 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.16 % Allowed : 13.69 % Favored : 84.14 % 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: 1.66 (0.33), residues: 619 helix: 2.00 (0.28), residues: 334 sheet: -0.96 (0.96), residues: 11 loop : 0.14 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.002 PHE I 110 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: I 28 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7184 (ppt170) outliers start: 12 outliers final: 4 residues processed: 101 average time/residue: 1.4145 time to fit residues: 148.3836 Evaluate side-chains 93 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.188145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.156411 restraints weight = 24695.049| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.01 r_work: 0.3754 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5265 Z= 0.177 Angle : 0.569 9.278 7126 Z= 0.287 Chirality : 0.041 0.164 781 Planarity : 0.004 0.037 906 Dihedral : 7.214 67.711 716 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.16 % Allowed : 13.69 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.33), residues: 619 helix: 2.08 (0.28), residues: 334 sheet: -0.94 (0.94), residues: 11 loop : 0.22 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.002 PHE I 110 TYR 0.018 0.002 TYR I 2 ARG 0.004 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6710 (tp40) REVERT: I 28 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7164 (ppt170) outliers start: 12 outliers final: 4 residues processed: 101 average time/residue: 1.3736 time to fit residues: 144.1652 Evaluate side-chains 97 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.187049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.155417 restraints weight = 21645.257| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.37 r_work: 0.3744 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5265 Z= 0.209 Angle : 0.603 8.446 7126 Z= 0.305 Chirality : 0.042 0.134 781 Planarity : 0.005 0.038 906 Dihedral : 7.326 68.806 716 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.62 % Allowed : 14.59 % Favored : 83.78 % 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: 1.64 (0.33), residues: 619 helix: 1.89 (0.28), residues: 340 sheet: -0.80 (0.89), residues: 11 loop : 0.22 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.020 0.002 TYR I 2 ARG 0.005 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.594 Fit side-chains REVERT: I 18 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6751 (tp40) REVERT: I 28 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7253 (ppt170) outliers start: 9 outliers final: 4 residues processed: 97 average time/residue: 1.4139 time to fit residues: 142.5196 Evaluate side-chains 96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.185722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156251 restraints weight = 18528.834| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.25 r_work: 0.3742 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5265 Z= 0.267 Angle : 0.669 9.074 7126 Z= 0.337 Chirality : 0.044 0.143 781 Planarity : 0.005 0.044 906 Dihedral : 7.512 69.513 716 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.98 % Allowed : 14.05 % Favored : 83.96 % 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: 1.43 (0.33), residues: 619 helix: 1.68 (0.28), residues: 340 sheet: -0.38 (0.92), residues: 11 loop : 0.14 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.022 0.002 TYR I 2 ARG 0.004 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.658 Fit side-chains REVERT: I 18 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6705 (tp40) REVERT: I 28 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7296 (ppt170) outliers start: 11 outliers final: 4 residues processed: 99 average time/residue: 1.4043 time to fit residues: 144.5211 Evaluate side-chains 97 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.185957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154217 restraints weight = 21677.397| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.26 r_work: 0.3734 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5265 Z= 0.255 Angle : 0.656 9.537 7126 Z= 0.335 Chirality : 0.044 0.140 781 Planarity : 0.005 0.045 906 Dihedral : 7.481 69.324 716 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 14.59 % Favored : 83.42 % 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: 1.40 (0.33), residues: 619 helix: 1.66 (0.28), residues: 340 sheet: -0.25 (0.95), residues: 11 loop : 0.11 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.021 0.002 TYR I 2 ARG 0.005 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.570 Fit side-chains REVERT: I 18 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6714 (tp40) REVERT: I 28 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7375 (ppt170) outliers start: 11 outliers final: 4 residues processed: 96 average time/residue: 1.3987 time to fit residues: 139.5116 Evaluate side-chains 96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.187176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155065 restraints weight = 21564.889| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.34 r_work: 0.3752 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 5265 Z= 0.214 Angle : 0.646 10.028 7126 Z= 0.327 Chirality : 0.043 0.217 781 Planarity : 0.005 0.043 906 Dihedral : 7.373 68.636 716 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 15.32 % Favored : 82.88 % 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: 1.59 (0.33), residues: 619 helix: 1.81 (0.28), residues: 340 sheet: -0.17 (0.96), residues: 11 loop : 0.21 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.019 0.002 TYR I 2 ARG 0.006 0.000 ARG I 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6703 (tp40) REVERT: I 28 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7369 (ppt170) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 1.4304 time to fit residues: 145.5874 Evaluate side-chains 96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.0020 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 HIS I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 172 GLN J 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.190055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.158829 restraints weight = 24162.493| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.94 r_work: 0.3780 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5265 Z= 0.161 Angle : 0.601 10.082 7126 Z= 0.301 Chirality : 0.041 0.139 781 Planarity : 0.005 0.039 906 Dihedral : 7.053 65.335 716 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 15.32 % Favored : 83.06 % 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: 1.92 (0.34), residues: 619 helix: 2.11 (0.28), residues: 340 sheet: -0.47 (0.91), residues: 11 loop : 0.34 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.019 0.001 PHE I 110 TYR 0.015 0.001 TYR I 91 ARG 0.007 0.000 ARG I 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7143.55 seconds wall clock time: 126 minutes 21.34 seconds (7581.34 seconds total)