Starting phenix.real_space_refine on Thu Mar 6 07:10:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6x_17510/03_2025/8p6x_17510.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6x_17510/03_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_17510/03_2025/8p6x_17510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6x_17510/03_2025/8p6x_17510.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6x_17510/03_2025/8p6x_17510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6x_17510/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.64, per 1000 atoms: 0.88 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: 1.48 Conformation dependent library (CDL) restraints added in 624.2 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: 0.56 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: 1.36 Time building geometry restraints manager: 1.70 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.940 Find NCS groups from input model: 0.070 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- 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 : 0.626 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: 1.3763 time to fit residues: 142.8941 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 : 0.576 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.4272 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.190196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158999 restraints weight = 20432.568| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.29 r_work: 0.3798 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0740 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= 0.142 Angle : 0.517 6.884 7126 Z= 0.263 Chirality : 0.039 0.125 781 Planarity : 0.004 0.038 906 Dihedral : 7.260 65.123 720 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.38 % 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: 2.11 (0.34), residues: 619 helix: 2.39 (0.29), residues: 334 sheet: -0.80 (1.26), residues: 18 loop : 0.37 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.007 0.001 HIS J 259 PHE 0.014 0.001 PHE I 110 TYR 0.017 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 104 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.680 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 103 average time/residue: 1.3798 time to fit residues: 147.5480 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 : 0.637 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.184564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155229 restraints weight = 16978.337| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.17 r_work: 0.3729 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5265 Z= 0.347 Angle : 0.705 7.795 7126 Z= 0.359 Chirality : 0.046 0.153 781 Planarity : 0.006 0.036 906 Dihedral : 7.657 69.638 716 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.16 % Allowed : 12.07 % Favored : 85.77 % 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: 1.31 (0.32), residues: 619 helix: 1.69 (0.28), residues: 332 sheet: -1.23 (1.08), residues: 11 loop : 0.03 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.018 0.003 PHE I 110 TYR 0.026 0.003 TYR I 2 ARG 0.005 0.001 ARG I 77 *********************** 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 110 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.576 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 1.4426 time to fit residues: 156.9300 Evaluate side-chains 96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 136 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 = 0.4233 r_free = 0.4233 target = 0.184446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154388 restraints weight = 21045.857| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.45 r_work: 0.3712 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.006 0.044 5265 Z= 0.349 Angle : 0.699 7.521 7126 Z= 0.359 Chirality : 0.046 0.149 781 Planarity : 0.005 0.036 906 Dihedral : 7.684 69.726 716 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 3.06 % Allowed : 12.25 % 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: 0.97 (0.32), residues: 619 helix: 1.37 (0.27), residues: 334 sheet: -0.53 (0.95), residues: 11 loop : -0.12 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.020 0.003 PHE I 110 TYR 0.025 0.003 TYR I 2 ARG 0.005 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 109 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.568 Fit side-chains REVERT: I 18 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6755 (tp40) REVERT: I 28 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7366 (ppt170) outliers start: 17 outliers final: 5 residues processed: 101 average time/residue: 1.3289 time to fit residues: 139.5729 Evaluate side-chains 95 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 227 GLU 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: 2.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 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 = 0.186072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154393 restraints weight = 21621.821| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.45 r_work: 0.3724 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5265 Z= 0.234 Angle : 0.619 8.040 7126 Z= 0.315 Chirality : 0.043 0.209 781 Planarity : 0.005 0.037 906 Dihedral : 7.464 69.200 716 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.52 % Allowed : 12.61 % Favored : 84.86 % 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: 1.70 (0.28), residues: 334 sheet: -0.29 (0.97), residues: 11 loop : 0.02 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.007 0.001 HIS I 161 PHE 0.020 0.002 PHE I 110 TYR 0.021 0.002 TYR I 2 ARG 0.003 0.001 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 109 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.632 Fit side-chains REVERT: I 18 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6747 (tp40) REVERT: I 28 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7388 (ppt170) outliers start: 14 outliers final: 4 residues processed: 102 average time/residue: 1.3804 time to fit residues: 146.2933 Evaluate side-chains 95 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.184247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154097 restraints weight = 24491.960| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.80 r_work: 0.3705 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.005 0.042 5265 Z= 0.332 Angle : 0.707 8.850 7126 Z= 0.360 Chirality : 0.046 0.148 781 Planarity : 0.006 0.040 906 Dihedral : 7.687 70.024 716 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 1.80 % Allowed : 13.15 % 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: 1.07 (0.32), residues: 619 helix: 1.43 (0.27), residues: 334 sheet: 0.32 (1.02), residues: 11 loop : -0.10 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.020 0.003 PHE I 110 TYR 0.025 0.003 TYR I 2 ARG 0.005 0.001 ARG I 77 *********************** 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 102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.578 Fit side-chains REVERT: I 18 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6760 (tp40) REVERT: I 28 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7390 (ppt170) outliers start: 10 outliers final: 4 residues processed: 96 average time/residue: 1.2989 time to fit residues: 129.7098 Evaluate side-chains 93 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 = 0.4255 r_free = 0.4255 target = 0.186961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155116 restraints weight = 21580.411| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.41 r_work: 0.3748 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5265 Z= 0.192 Angle : 0.602 9.352 7126 Z= 0.303 Chirality : 0.042 0.134 781 Planarity : 0.005 0.038 906 Dihedral : 7.331 68.370 716 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.80 % Allowed : 13.51 % 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: 1.57 (0.33), residues: 619 helix: 1.88 (0.28), residues: 334 sheet: -0.25 (0.89), residues: 11 loop : 0.14 (0.37), residues: 274 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 0.021 0.002 PHE I 110 TYR 0.019 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 104 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6710 (tp40) REVERT: I 28 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7332 (ppt170) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 1.5222 time to fit residues: 156.3202 Evaluate side-chains 93 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.185031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155023 restraints weight = 18579.399| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.21 r_work: 0.3735 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.134 | | 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: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5265 Z= 0.283 Angle : 0.691 10.057 7126 Z= 0.347 Chirality : 0.045 0.143 781 Planarity : 0.005 0.044 906 Dihedral : 7.573 69.626 716 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 2.34 % Allowed : 13.51 % 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: 1.27 (0.33), residues: 619 helix: 1.57 (0.28), residues: 340 sheet: -0.51 (0.96), residues: 11 loop : 0.05 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.020 0.002 PHE I 110 TYR 0.024 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 102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6695 (tp40) REVERT: I 28 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7247 (ppt170) outliers start: 13 outliers final: 5 residues processed: 94 average time/residue: 1.4559 time to fit residues: 142.0729 Evaluate side-chains 93 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 I residue 236 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: 0.9990 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.185805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154687 restraints weight = 21920.393| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.46 r_work: 0.3734 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.004 0.068 5265 Z= 0.249 Angle : 0.675 10.703 7126 Z= 0.339 Chirality : 0.044 0.137 781 Planarity : 0.005 0.043 906 Dihedral : 7.492 69.231 716 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 14.59 % Favored : 83.60 % 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: 1.34 (0.33), residues: 619 helix: 1.61 (0.28), residues: 340 sheet: -0.46 (0.99), residues: 11 loop : 0.11 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.020 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 99 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 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: 0.7559 (OUTLIER) cc_final: 0.7324 (ppt170) outliers start: 10 outliers final: 5 residues processed: 94 average time/residue: 1.4391 time to fit residues: 140.5014 Evaluate side-chains 94 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 I residue 236 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: 0.8980 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 0.0470 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.186522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156073 restraints weight = 21577.806| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.47 r_work: 0.3739 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5265 Z= 0.220 Angle : 0.649 11.190 7126 Z= 0.328 Chirality : 0.043 0.135 781 Planarity : 0.005 0.043 906 Dihedral : 7.405 68.702 716 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 14.95 % 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: 1.47 (0.33), residues: 619 helix: 1.73 (0.28), residues: 340 sheet: -0.55 (0.94), residues: 11 loop : 0.15 (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 I 161 PHE 0.020 0.002 PHE I 110 TYR 0.020 0.002 TYR I 2 ARG 0.006 0.001 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 101 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6733 (tp40) REVERT: I 28 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7333 (ppt170) outliers start: 11 outliers final: 4 residues processed: 95 average time/residue: 1.3900 time to fit residues: 137.1538 Evaluate side-chains 94 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 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: 3.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.188327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156492 restraints weight = 23993.100| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.94 r_work: 0.3749 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 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 = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1286 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= 0.181 Angle : 0.627 11.204 7126 Z= 0.316 Chirality : 0.042 0.176 781 Planarity : 0.005 0.039 906 Dihedral : 7.214 67.035 716 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.08 % Allowed : 15.86 % 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: 1.73 (0.33), residues: 619 helix: 1.97 (0.28), residues: 340 sheet: -0.83 (0.89), residues: 11 loop : 0.25 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.021 0.002 PHE I 110 TYR 0.017 0.002 TYR I 2 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: 7286.13 seconds wall clock time: 124 minutes 6.73 seconds (7446.73 seconds total)