Starting phenix.real_space_refine on Fri Jul 19 00:56:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/07_2024/8p6x_17510.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/07_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_17510/07_2024/8p6x_17510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/07_2024/8p6x_17510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/07_2024/8p6x_17510.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/07_2024/8p6x_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 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-5388/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: 4.11, per 1000 atoms: 0.78 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: 2.40 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.41 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 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 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 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 ========== 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: 2.380 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.400 Find NCS groups from input model: 0.070 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:15.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 5265 Z= 0.304 Angle : 0.628 9.294 7126 Z= 0.295 Chirality : 0.042 0.186 781 Planarity : 0.004 0.036 906 Dihedral : 16.385 87.437 1980 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 0.72 % Allowed : 14.23 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.34), residues: 619 helix: 1.92 (0.28), residues: 336 sheet: 0.02 (1.52), residues: 18 loop : 0.29 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.005 0.001 HIS J 258 PHE 0.016 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.006 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.611 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: 1.7490 time to fit residues: 181.7495 Evaluate side-chains 92 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5265 Z= 0.131 Angle : 0.500 7.026 7126 Z= 0.254 Chirality : 0.039 0.124 781 Planarity : 0.004 0.038 906 Dihedral : 7.206 64.521 720 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.38 % Rotamer: Outliers : 1.26 % Allowed : 14.05 % 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: 2.18 (0.34), residues: 619 helix: 2.45 (0.29), residues: 334 sheet: -0.87 (1.23), residues: 18 loop : 0.39 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 11 HIS 0.008 0.001 HIS J 259 PHE 0.014 0.001 PHE I 110 TYR 0.015 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 fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.550 Fit side-chains REVERT: I 66 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6873 (tp30) outliers start: 7 outliers final: 1 residues processed: 102 average time/residue: 1.3032 time to fit residues: 138.2297 Evaluate side-chains 94 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 66 GLU 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: 5.9990 chunk 17 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.022 5265 Z= 0.158 Angle : 0.527 7.658 7126 Z= 0.266 Chirality : 0.040 0.128 781 Planarity : 0.004 0.037 906 Dihedral : 7.113 66.439 716 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % 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: 2.09 (0.34), residues: 619 helix: 2.37 (0.28), residues: 335 sheet: -0.92 (1.15), residues: 18 loop : 0.34 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.017 0.002 TYR I 2 ARG 0.003 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.550 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 1.3729 time to fit residues: 139.7273 Evaluate side-chains 94 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5265 Z= 0.155 Angle : 0.530 7.817 7126 Z= 0.265 Chirality : 0.040 0.127 781 Planarity : 0.004 0.037 906 Dihedral : 7.116 66.625 716 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.45 % Favored : 98.38 % Rotamer: Outliers : 1.80 % Allowed : 13.69 % Favored : 84.50 % 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: 2.08 (0.34), residues: 619 helix: 2.36 (0.28), residues: 335 sheet: -0.99 (1.13), residues: 18 loop : 0.35 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.014 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.003 0.000 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 104 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.551 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 100 average time/residue: 1.3148 time to fit residues: 136.6461 Evaluate side-chains 94 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 0.2980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5265 Z= 0.206 Angle : 0.590 8.212 7126 Z= 0.296 Chirality : 0.042 0.136 781 Planarity : 0.004 0.036 906 Dihedral : 7.373 68.820 716 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 14.05 % 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: 1.83 (0.33), residues: 619 helix: 2.12 (0.28), residues: 335 sheet: -1.10 (1.10), residues: 11 loop : 0.24 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 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 108 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.627 Fit side-chains REVERT: I 18 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6492 (tp40) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 1.3669 time to fit residues: 146.2014 Evaluate side-chains 98 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5265 Z= 0.195 Angle : 0.587 9.754 7126 Z= 0.294 Chirality : 0.041 0.132 781 Planarity : 0.004 0.036 906 Dihedral : 7.335 68.649 716 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.80 % Allowed : 13.69 % Favored : 84.50 % 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: 1.76 (0.33), residues: 619 helix: 2.08 (0.28), residues: 335 sheet: -1.04 (1.02), residues: 11 loop : 0.19 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.015 0.002 PHE I 110 TYR 0.018 0.002 TYR I 2 ARG 0.004 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.646 Fit side-chains REVERT: I 18 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6485 (tp40) REVERT: I 28 ARG cc_start: 0.7368 (ppt170) cc_final: 0.7166 (ppt170) REVERT: I 138 LYS cc_start: 0.7343 (ptpp) cc_final: 0.7120 (ptpt) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 1.4383 time to fit residues: 152.4042 Evaluate side-chains 96 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5265 Z= 0.291 Angle : 0.686 11.162 7126 Z= 0.345 Chirality : 0.045 0.144 781 Planarity : 0.005 0.042 906 Dihedral : 7.621 69.794 716 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.98 % Allowed : 15.14 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.33), residues: 619 helix: 1.69 (0.27), residues: 339 sheet: -0.52 (0.92), residues: 11 loop : -0.00 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.023 0.003 TYR I 2 ARG 0.004 0.001 ARG I 28 *********************** 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 105 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.605 Fit side-chains REVERT: I 18 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6518 (tp40) REVERT: I 138 LYS cc_start: 0.7346 (ptpp) cc_final: 0.7134 (ptpt) outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 1.3657 time to fit residues: 142.0172 Evaluate side-chains 97 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5265 Z= 0.177 Angle : 0.578 10.303 7126 Z= 0.292 Chirality : 0.041 0.134 781 Planarity : 0.004 0.037 906 Dihedral : 7.288 68.042 716 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 15.68 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.33), residues: 619 helix: 2.04 (0.28), residues: 334 sheet: -0.55 (0.86), residues: 11 loop : 0.15 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS J 258 PHE 0.017 0.002 PHE I 110 TYR 0.017 0.002 TYR I 2 ARG 0.006 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 103 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.621 Fit side-chains REVERT: I 18 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6484 (tp40) REVERT: I 138 LYS cc_start: 0.7332 (ptpp) cc_final: 0.7123 (ptpt) outliers start: 9 outliers final: 4 residues processed: 98 average time/residue: 1.4241 time to fit residues: 144.9734 Evaluate side-chains 94 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5265 Z= 0.235 Angle : 0.652 12.623 7126 Z= 0.327 Chirality : 0.044 0.208 781 Planarity : 0.005 0.046 906 Dihedral : 7.480 69.233 716 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 15.14 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.33), residues: 619 helix: 1.85 (0.28), residues: 341 sheet: -0.28 (0.90), residues: 11 loop : 0.08 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.016 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 102 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.501 Fit side-chains REVERT: I 18 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6515 (tp40) REVERT: I 138 LYS cc_start: 0.7347 (ptpp) cc_final: 0.7137 (ptpt) REVERT: I 229 GLU cc_start: 0.6826 (pm20) cc_final: 0.6540 (pp20) outliers start: 11 outliers final: 4 residues processed: 96 average time/residue: 1.3641 time to fit residues: 136.0045 Evaluate side-chains 94 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 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 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5265 Z= 0.189 Angle : 0.619 11.418 7126 Z= 0.310 Chirality : 0.042 0.137 781 Planarity : 0.005 0.041 906 Dihedral : 7.298 67.923 716 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 15.50 % Favored : 83.24 % 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: 1.98 (0.28), residues: 340 sheet: -0.39 (0.89), residues: 11 loop : 0.16 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.017 0.002 TYR I 2 ARG 0.006 0.000 ARG I 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.554 Fit side-chains REVERT: I 18 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6486 (tp40) REVERT: I 138 LYS cc_start: 0.7336 (ptpp) cc_final: 0.7129 (ptpt) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 1.3722 time to fit residues: 133.8618 Evaluate side-chains 94 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.184683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154259 restraints weight = 20779.733| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.44 r_work: 0.3726 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 5265 Z= 0.293 Angle : 0.728 13.066 7126 Z= 0.363 Chirality : 0.046 0.145 781 Planarity : 0.005 0.049 906 Dihedral : 7.627 69.464 716 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.44 % Allowed : 15.86 % Favored : 82.70 % 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: 1.36 (0.33), residues: 619 helix: 1.65 (0.27), residues: 341 sheet: 0.02 (0.94), residues: 11 loop : 0.05 (0.38), residues: 267 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 0.016 0.002 PHE I 30 TYR 0.022 0.003 TYR I 2 ARG 0.005 0.001 ARG I 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3052.66 seconds wall clock time: 53 minutes 58.51 seconds (3238.51 seconds total)