Starting phenix.real_space_refine on Fri Aug 2 21:04:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/08_2024/8p6x_17510.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/08_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_17510/08_2024/8p6x_17510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/08_2024/8p6x_17510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/08_2024/8p6x_17510.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6x_17510/08_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-5409/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: 4.66, per 1000 atoms: 0.88 Number of scatterers: 5284 At special positions: 0 Unit cell: (84.7875, 94.05, 67.6875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1063 8.00 N 875 7.00 C 3315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.96 Conformation dependent library (CDL) restraints added in 1.1 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: 0.55 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: 1.37 Time building geometry restraints manager: 3.15 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 3.040 nonbonded pdb=" O HOH J 501 " pdb=" O HOH J 550 " model vdw 2.230 3.040 nonbonded pdb=" O LEU I 236 " pdb=" O HOH I 401 " model vdw 2.244 3.040 nonbonded pdb=" O HOH J 555 " pdb=" O HOH J 560 " model vdw 2.258 3.040 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 402 " model vdw 2.262 3.040 ... (remaining 47456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- 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 : 0.661 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: 1.5003 time to fit residues: 155.7038 Evaluate side-chains 92 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 236 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 48 optimal weight: 0.0370 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 0.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 258 HIS J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5265 Z= 0.139 Angle : 0.511 6.835 7126 Z= 0.260 Chirality : 0.039 0.125 781 Planarity : 0.004 0.038 906 Dihedral : 7.212 64.496 720 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 13.51 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.34), residues: 619 helix: 2.42 (0.28), residues: 334 sheet: -0.84 (1.24), residues: 18 loop : 0.38 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 132 HIS 0.007 0.001 HIS J 259 PHE 0.014 0.001 PHE I 110 TYR 0.016 0.001 TYR I 91 ARG 0.004 0.000 ARG J 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.952 Fit side-chains REVERT: I 66 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6869 (tp30) outliers start: 8 outliers final: 1 residues processed: 105 average time/residue: 1.4142 time to fit residues: 154.7029 Evaluate side-chains 91 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1011 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= 0.149 Angle : 0.516 7.438 7126 Z= 0.261 Chirality : 0.040 0.127 781 Planarity : 0.004 0.038 906 Dihedral : 7.044 65.732 716 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 13.69 % 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: 2.05 (0.34), residues: 619 helix: 2.35 (0.28), residues: 334 sheet: -0.96 (1.15), residues: 18 loop : 0.34 (0.38), residues: 267 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 0.017 0.002 TYR I 91 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 100 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.673 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 98 average time/residue: 1.6012 time to fit residues: 163.4039 Evaluate side-chains 90 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.0370 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0978 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= 0.197 Angle : 0.570 7.468 7126 Z= 0.287 Chirality : 0.041 0.134 781 Planarity : 0.005 0.036 906 Dihedral : 7.277 68.398 716 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.16 % Allowed : 12.43 % 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: 1.87 (0.33), residues: 619 helix: 2.15 (0.28), residues: 335 sheet: -1.25 (1.19), residues: 11 loop : 0.28 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.019 0.002 TYR I 2 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 106 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.641 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 103 average time/residue: 1.4076 time to fit residues: 150.5674 Evaluate side-chains 92 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 242 ARG 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: 0.1980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 HIS I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5265 Z= 0.251 Angle : 0.631 9.041 7126 Z= 0.318 Chirality : 0.043 0.141 781 Planarity : 0.005 0.036 906 Dihedral : 7.440 69.319 716 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.98 % Allowed : 13.33 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.33), residues: 619 helix: 1.85 (0.28), residues: 341 sheet: -1.16 (1.06), residues: 11 loop : 0.12 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.022 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 106 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.666 Fit side-chains REVERT: I 18 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: I 138 LYS cc_start: 0.7344 (ptpp) cc_final: 0.7136 (ptpp) outliers start: 11 outliers final: 4 residues processed: 101 average time/residue: 1.3397 time to fit residues: 140.7152 Evaluate side-chains 96 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 136 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5265 Z= 0.330 Angle : 0.704 8.760 7126 Z= 0.356 Chirality : 0.046 0.149 781 Planarity : 0.005 0.040 906 Dihedral : 7.637 69.892 716 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.98 % Allowed : 13.87 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.32), residues: 619 helix: 1.48 (0.27), residues: 341 sheet: -0.58 (0.93), residues: 11 loop : -0.02 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 PHE 0.017 0.003 PHE I 30 TYR 0.024 0.003 TYR I 2 ARG 0.005 0.001 ARG I 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6516 (tp40) REVERT: I 28 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7098 (ppt170) REVERT: I 138 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7160 (ptpt) outliers start: 11 outliers final: 4 residues processed: 101 average time/residue: 1.3233 time to fit residues: 138.8876 Evaluate side-chains 97 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 138 LYS 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: 0.6980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5265 Z= 0.200 Angle : 0.596 9.463 7126 Z= 0.303 Chirality : 0.042 0.134 781 Planarity : 0.005 0.037 906 Dihedral : 7.345 68.702 716 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 14.95 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.33), residues: 619 helix: 1.82 (0.28), residues: 340 sheet: -0.60 (0.88), residues: 11 loop : 0.13 (0.37), residues: 268 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 0.019 0.002 TYR I 2 ARG 0.005 0.000 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.649 Fit side-chains REVERT: I 18 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6509 (tp40) REVERT: I 28 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7106 (ppt170) outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 1.3666 time to fit residues: 140.7088 Evaluate side-chains 96 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5265 Z= 0.172 Angle : 0.578 9.969 7126 Z= 0.292 Chirality : 0.041 0.164 781 Planarity : 0.004 0.036 906 Dihedral : 7.174 67.107 716 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.98 % Allowed : 14.59 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.33), residues: 619 helix: 2.04 (0.28), residues: 340 sheet: -0.61 (0.86), residues: 11 loop : 0.24 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.006 0.001 HIS J 258 PHE 0.018 0.002 PHE I 110 TYR 0.017 0.002 TYR I 91 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 107 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6486 (tp40) REVERT: I 28 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6922 (ppt170) outliers start: 11 outliers final: 4 residues processed: 102 average time/residue: 1.3091 time to fit residues: 138.9128 Evaluate side-chains 96 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 142 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5265 Z= 0.279 Angle : 0.690 10.672 7126 Z= 0.348 Chirality : 0.045 0.143 781 Planarity : 0.005 0.048 906 Dihedral : 7.513 69.360 716 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 14.95 % 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: 1.44 (0.33), residues: 619 helix: 1.71 (0.28), residues: 340 sheet: -0.20 (0.96), residues: 11 loop : 0.12 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.017 0.002 PHE I 110 TYR 0.023 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 100 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: I 18 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6524 (tp40) REVERT: I 28 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6987 (ppt170) REVERT: I 138 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.7135 (ptpp) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 1.3936 time to fit residues: 136.2233 Evaluate side-chains 96 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 259 HIS Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 28 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 138 LYS 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0472 > 50: distance: 95 - 99: 24.683 distance: 99 - 100: 12.793 distance: 100 - 101: 29.837 distance: 100 - 103: 49.624 distance: 101 - 102: 18.299 distance: 101 - 108: 22.446 distance: 103 - 104: 38.515 distance: 104 - 105: 40.503 distance: 105 - 106: 33.865 distance: 106 - 107: 27.277 distance: 108 - 109: 17.230 distance: 109 - 110: 18.446 distance: 109 - 112: 7.184 distance: 110 - 111: 27.276 distance: 110 - 120: 23.753 distance: 112 - 113: 20.844 distance: 113 - 114: 12.130 distance: 113 - 115: 12.830 distance: 114 - 116: 22.713 distance: 115 - 117: 18.372 distance: 116 - 118: 8.834 distance: 117 - 118: 7.734 distance: 118 - 119: 20.017 distance: 120 - 121: 7.997 distance: 121 - 122: 39.589 distance: 121 - 124: 35.467 distance: 122 - 123: 18.961 distance: 122 - 131: 17.542 distance: 124 - 125: 43.611 distance: 125 - 126: 12.322 distance: 125 - 127: 20.926 distance: 126 - 128: 38.863 distance: 127 - 129: 37.042 distance: 128 - 130: 20.681 distance: 129 - 130: 37.065 distance: 131 - 132: 39.860 distance: 132 - 133: 45.678 distance: 132 - 135: 24.835 distance: 133 - 134: 16.465 distance: 133 - 137: 26.289 distance: 135 - 136: 41.033 distance: 137 - 138: 26.240 distance: 138 - 139: 15.816 distance: 138 - 141: 22.692 distance: 139 - 140: 27.600 distance: 139 - 145: 37.140 distance: 141 - 142: 24.022 distance: 142 - 143: 22.539 distance: 142 - 144: 9.989 distance: 145 - 146: 3.608 distance: 146 - 147: 31.829 distance: 146 - 149: 36.765 distance: 147 - 148: 53.609 distance: 147 - 156: 27.666 distance: 149 - 150: 45.714 distance: 150 - 151: 38.643 distance: 151 - 152: 38.441 distance: 152 - 153: 19.923 distance: 153 - 154: 12.597 distance: 153 - 155: 17.029 distance: 156 - 157: 35.180 distance: 156 - 162: 47.864 distance: 157 - 158: 55.691 distance: 157 - 160: 33.498 distance: 158 - 159: 56.043 distance: 158 - 163: 51.392 distance: 160 - 161: 29.472 distance: 161 - 162: 9.881 distance: 163 - 164: 41.472 distance: 164 - 165: 40.401 distance: 165 - 166: 19.624 distance: 165 - 167: 18.708 distance: 167 - 168: 8.051 distance: 167 - 173: 14.945 distance: 168 - 169: 34.310 distance: 168 - 171: 53.398 distance: 169 - 170: 18.544 distance: 169 - 174: 14.935 distance: 171 - 172: 26.404 distance: 172 - 173: 36.306 distance: 174 - 175: 44.871 distance: 175 - 176: 37.608 distance: 175 - 178: 13.529 distance: 176 - 177: 52.053 distance: 176 - 181: 20.124 distance: 178 - 179: 20.466 distance: 178 - 180: 46.127