Starting phenix.real_space_refine on Fri Apr 5 20:17:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/04_2024/8p6x_17510_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/04_2024/8p6x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/04_2024/8p6x_17510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/04_2024/8p6x_17510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/04_2024/8p6x_17510_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/04_2024/8p6x_17510_updated.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 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 Residue "I GLU 16": "OE1" <-> "OE2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I ASP 250": "OD1" <-> "OD2" Residue "I GLU 278": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.59, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 997.5 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... running ksdssp... Secondary structure from input PDB file: 32 helices and 2 sheets defined 51.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 284 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 37 Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.685A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.949A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.674A 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 177 Processing helix chain 'I' and resid 184 through 200 removed outlier: 4.476A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 242 through 260 Processing helix chain 'I' and resid 267 through 283 removed outlier: 3.582A pdb=" N VAL I 272 " --> pdb=" O GLU I 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 67 Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 192 through 208 removed outlier: 4.020A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 229 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 77 through 83 removed outlier: 6.667A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 214 hydrogen bonds defined for protein. 561 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: 1.34 Time building geometry restraints manager: 2.45 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: 97.23 - 104.57: 106 104.57 - 111.92: 2528 111.92 - 119.26: 1767 119.26 - 126.60: 2643 126.60 - 133.95: 82 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: 688 2.75 - 3.29: 5503 3.29 - 3.82: 10036 3.82 - 4.36: 12046 4.36 - 4.90: 19420 Nonbonded interactions: 47693 Sorted by model distance: nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.211 2.440 nonbonded pdb=" O HOH J 501 " pdb=" O HOH J 550 " model vdw 2.230 2.440 nonbonded pdb=" O LEU I 236 " pdb=" O HOH I 401 " model vdw 2.244 2.440 nonbonded pdb=" O HOH J 555 " pdb=" O HOH J 560 " model vdw 2.258 2.440 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 402 " model vdw 2.262 2.440 ... (remaining 47688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 9.380 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: 0.020 Extract box with map and model: 12.950 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.980 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.030 ------------------------------------------------------------------------------- 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= 0.300 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 fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.665 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: 1.4648 time to fit residues: 151.6248 Evaluate side-chains 92 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 0.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 48 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN J 130 GLN ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.0448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5265 Z= 0.122 Angle : 0.462 7.106 7126 Z= 0.232 Chirality : 0.038 0.127 781 Planarity : 0.004 0.039 906 Dihedral : 7.123 64.225 720 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 13.87 % 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: 1.96 (0.34), residues: 619 helix: 2.14 (0.28), residues: 336 sheet: -0.19 (1.42), residues: 18 loop : 0.40 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 11 HIS 0.005 0.001 HIS J 258 PHE 0.014 0.001 PHE I 110 TYR 0.014 0.001 TYR I 91 ARG 0.006 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 fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.618 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 102 average time/residue: 1.4375 time to fit residues: 152.2885 Evaluate side-chains 90 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0414 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= 0.149 Angle : 0.494 7.200 7126 Z= 0.246 Chirality : 0.039 0.129 781 Planarity : 0.004 0.038 906 Dihedral : 7.034 66.269 716 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 12.61 % Favored : 85.41 % 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: 1.96 (0.34), residues: 619 helix: 2.13 (0.28), residues: 336 sheet: -0.11 (1.45), residues: 18 loop : 0.41 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 132 HIS 0.005 0.001 HIS J 258 PHE 0.014 0.001 PHE I 30 TYR 0.016 0.001 TYR I 91 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 105 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.665 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 101 average time/residue: 1.3228 time to fit residues: 138.9969 Evaluate side-chains 93 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5265 Z= 0.217 Angle : 0.573 7.558 7126 Z= 0.286 Chirality : 0.041 0.135 781 Planarity : 0.004 0.035 906 Dihedral : 7.358 68.704 716 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.34 % Allowed : 12.07 % Favored : 85.59 % 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: 1.62 (0.33), residues: 619 helix: 1.80 (0.28), residues: 342 sheet: -0.78 (1.50), residues: 11 loop : 0.31 (0.38), residues: 266 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 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.003 0.001 ARG I 21 *********************** 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 fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.646 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 106 average time/residue: 1.3499 time to fit residues: 148.6477 Evaluate side-chains 94 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5265 Z= 0.265 Angle : 0.624 8.971 7126 Z= 0.311 Chirality : 0.043 0.138 781 Planarity : 0.005 0.034 906 Dihedral : 7.518 69.397 716 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 13.51 % 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: 1.34 (0.33), residues: 619 helix: 1.57 (0.28), residues: 342 sheet: -0.58 (1.48), residues: 11 loop : 0.17 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 ARG 0.003 0.001 ARG I 77 *********************** 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 105 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.678 Fit side-chains REVERT: I 28 ARG cc_start: 0.7376 (ppt170) cc_final: 0.7086 (ppt170) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 1.4795 time to fit residues: 155.1433 Evaluate side-chains 96 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5265 Z= 0.244 Angle : 0.612 8.763 7126 Z= 0.306 Chirality : 0.042 0.137 781 Planarity : 0.005 0.034 906 Dihedral : 7.489 69.458 716 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.16 % Allowed : 13.51 % Favored : 84.32 % 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: 1.28 (0.33), residues: 619 helix: 1.52 (0.28), residues: 342 sheet: -0.56 (1.45), residues: 11 loop : 0.14 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 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 0.004 0.001 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 109 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.593 Fit side-chains REVERT: I 28 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7083 (ppt170) outliers start: 12 outliers final: 4 residues processed: 103 average time/residue: 1.4099 time to fit residues: 150.8696 Evaluate side-chains 98 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5265 Z= 0.189 Angle : 0.559 9.594 7126 Z= 0.281 Chirality : 0.040 0.132 781 Planarity : 0.004 0.035 906 Dihedral : 7.307 68.735 716 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 2.52 % Allowed : 13.69 % 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: 1.50 (0.33), residues: 619 helix: 1.72 (0.28), residues: 342 sheet: -0.57 (1.46), residues: 11 loop : 0.22 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.005 0.001 HIS J 258 PHE 0.017 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 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 109 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.621 Fit side-chains REVERT: I 28 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7072 (ppt170) outliers start: 14 outliers final: 4 residues processed: 101 average time/residue: 1.4012 time to fit residues: 146.9305 Evaluate side-chains 95 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5265 Z= 0.184 Angle : 0.573 11.985 7126 Z= 0.284 Chirality : 0.041 0.172 781 Planarity : 0.004 0.036 906 Dihedral : 7.249 68.138 716 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 1.44 % Allowed : 14.23 % Favored : 84.32 % 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: 1.78 (0.28), residues: 342 sheet: -0.56 (1.45), residues: 11 loop : 0.27 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 258 PHE 0.017 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.000 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 99 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.576 Fit side-chains REVERT: I 28 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7070 (ppt170) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 1.4333 time to fit residues: 141.3178 Evaluate side-chains 92 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.0483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5265 Z= 0.184 Angle : 0.578 10.956 7126 Z= 0.286 Chirality : 0.040 0.130 781 Planarity : 0.004 0.038 906 Dihedral : 7.218 67.887 716 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 1.44 % Allowed : 14.59 % 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: 1.70 (0.33), residues: 619 helix: 1.89 (0.28), residues: 336 sheet: -0.57 (1.45), residues: 11 loop : 0.33 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 258 PHE 0.017 0.002 PHE I 110 TYR 0.016 0.002 TYR I 91 ARG 0.006 0.000 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 98 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.661 Fit side-chains REVERT: I 28 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7066 (ppt170) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 1.4149 time to fit residues: 138.2066 Evaluate side-chains 93 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.2980 chunk 56 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** J 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5265 Z= 0.169 Angle : 0.587 13.214 7126 Z= 0.286 Chirality : 0.040 0.135 781 Planarity : 0.004 0.038 906 Dihedral : 7.052 66.292 716 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.26 % Allowed : 14.95 % 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: 1.87 (0.34), residues: 619 helix: 1.99 (0.28), residues: 336 sheet: 0.69 (1.49), residues: 17 loop : 0.40 (0.38), residues: 266 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 0.017 0.001 PHE I 110 TYR 0.014 0.001 TYR I 91 ARG 0.007 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 95 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.672 Fit side-chains REVERT: I 28 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7049 (ppt170) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 1.4688 time to fit residues: 138.6728 Evaluate side-chains 92 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 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 281 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.184417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154379 restraints weight = 20738.435| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.42 r_work: 0.3717 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 5265 Z= 0.368 Angle : 0.750 10.395 7126 Z= 0.378 Chirality : 0.047 0.163 781 Planarity : 0.006 0.050 906 Dihedral : 7.697 69.419 716 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % 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: 1.09 (0.33), residues: 619 helix: 1.34 (0.27), residues: 342 sheet: -0.37 (1.44), residues: 11 loop : 0.08 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.016 0.003 PHE I 30 TYR 0.020 0.003 TYR I 2 ARG 0.005 0.001 ARG I 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3140.63 seconds wall clock time: 56 minutes 52.80 seconds (3412.80 seconds total)