Starting phenix.real_space_refine on Fri Apr 5 20:13:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p76_17519/04_2024/8p76_17519_updated.pdb" } resolution = 2.0 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 3296 2.51 5 N 870 2.21 5 O 1064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 299": "OD1" <-> "OD2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I GLU 229": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J GLU 235": "OE1" <-> "OE2" Residue "J TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 270": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5261 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: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'X1W': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Time building chain proxies: 3.42, per 1000 atoms: 0.65 Number of scatterers: 5261 At special positions: 0 Unit cell: (84.7875, 93.3375, 68.4, 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 1064 8.00 N 870 7.00 C 3296 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: 2.04 Conformation dependent library (CDL) restraints added in 834.9 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 2 sheets defined 53.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'H' and resid 263 through 269 removed outlier: 4.553A pdb=" N GLY H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG H 268 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 285 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 35 Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 116 Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.926A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.706A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 Processing helix chain 'I' and resid 184 through 187 Processing helix chain 'I' and resid 189 through 200 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 242 through 260 Processing helix chain 'I' and resid 267 through 282 Processing helix chain 'J' and resid 57 through 66 Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 218 through 229 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 291 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 77 through 81 removed outlier: 6.869A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 213 hydrogen bonds defined for protein. 627 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: 1.28 Time building geometry restraints manager: 2.19 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: 1642 1.34 - 1.46: 1183 1.46 - 1.58: 2358 1.58 - 1.70: 3 1.70 - 1.82: 49 Bond restraints: 5235 Sorted by residual: bond pdb=" C20 X1W J 401 " pdb=" C24 X1W J 401 " ideal model delta sigma weight residual 1.340 1.621 -0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C23 X1W J 401 " pdb=" N22 X1W J 401 " ideal model delta sigma weight residual 1.355 1.476 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C23 X1W J 401 " pdb=" C24 X1W J 401 " ideal model delta sigma weight residual 1.662 1.549 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" C21 X1W J 401 " pdb=" N22 X1W J 401 " ideal model delta sigma weight residual 1.579 1.486 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C26 X1W J 401 " pdb=" C27 X1W J 401 " ideal model delta sigma weight residual 1.556 1.610 -0.054 2.00e-02 2.50e+03 7.25e+00 ... (remaining 5230 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.68: 136 105.68 - 112.74: 2729 112.74 - 119.80: 1744 119.80 - 126.86: 2402 126.86 - 133.92: 74 Bond angle restraints: 7085 Sorted by residual: angle pdb=" CG ARG I 279 " pdb=" CD ARG I 279 " pdb=" NE ARG I 279 " ideal model delta sigma weight residual 112.00 118.65 -6.65 2.20e+00 2.07e-01 9.15e+00 angle pdb=" C02 X1W J 401 " pdb=" C04 X1W J 401 " pdb=" C05 X1W J 401 " ideal model delta sigma weight residual 118.11 126.84 -8.73 3.00e+00 1.11e-01 8.46e+00 angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.42e+00 angle pdb=" CB MET I 237 " pdb=" CG MET I 237 " pdb=" SD MET I 237 " ideal model delta sigma weight residual 112.70 120.84 -8.14 3.00e+00 1.11e-01 7.35e+00 angle pdb=" C21 X1W J 401 " pdb=" C20 X1W J 401 " pdb=" N19 X1W J 401 " ideal model delta sigma weight residual 109.96 117.95 -7.99 3.00e+00 1.11e-01 7.09e+00 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.21: 2951 27.21 - 54.42: 176 54.42 - 81.64: 27 81.64 - 108.85: 3 108.85 - 136.06: 1 Dihedral angle restraints: 3158 sinusoidal: 1311 harmonic: 1847 Sorted by residual: dihedral pdb=" C08 X1W J 401 " pdb=" C10 X1W J 401 " pdb=" N09 X1W J 401 " pdb=" C11 X1W J 401 " ideal model delta sinusoidal sigma weight residual 202.33 66.27 136.06 1 3.00e+01 1.11e-03 1.83e+01 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 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+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 39.27 50.73 2 1.50e+01 4.44e-03 1.28e+01 ... (remaining 3155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 721 0.078 - 0.156: 55 0.156 - 0.234: 0 0.234 - 0.312: 0 0.312 - 0.390: 1 Chirality restraints: 777 Sorted by residual: chirality pdb=" C24 X1W J 401 " pdb=" C20 X1W J 401 " pdb=" C23 X1W J 401 " pdb=" O25 X1W J 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.90 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA MET I 237 " pdb=" N MET I 237 " pdb=" C MET I 237 " pdb=" CB MET I 237 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA MET J 94 " pdb=" N MET J 94 " pdb=" C MET J 94 " pdb=" CB MET J 94 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 774 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 116 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" CG ASP I 116 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP I 116 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP I 116 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 165 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO I 166 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO J 140 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.019 5.00e-02 4.00e+02 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1269 2.79 - 3.32: 5257 3.32 - 3.84: 9973 3.84 - 4.37: 11873 4.37 - 4.90: 18864 Nonbonded interactions: 47236 Sorted by model distance: nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 501 " model vdw 2.258 2.440 nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.261 2.440 nonbonded pdb=" O ARG I 89 " pdb=" O HOH I 401 " model vdw 2.287 2.440 nonbonded pdb=" O HOH J 504 " pdb=" O HOH J 549 " model vdw 2.304 2.440 nonbonded pdb=" O HOH J 554 " pdb=" O HOH J 557 " model vdw 2.306 2.440 ... (remaining 47231 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 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: 12.420 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.006 0.281 5235 Z= 0.361 Angle : 0.631 8.726 7085 Z= 0.301 Chirality : 0.042 0.390 777 Planarity : 0.004 0.036 904 Dihedral : 17.096 136.061 1962 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 16.43 % Favored : 82.67 % 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: 1.97 (0.34), residues: 618 helix: 2.09 (0.29), residues: 335 sheet: 2.90 (1.24), residues: 14 loop : 0.29 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.016 0.001 TYR I 60 ARG 0.009 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.642 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 103 average time/residue: 1.6185 time to fit residues: 172.1692 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5235 Z= 0.191 Angle : 0.562 7.027 7085 Z= 0.279 Chirality : 0.040 0.134 777 Planarity : 0.004 0.034 904 Dihedral : 9.202 134.807 707 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.17 % Allowed : 14.44 % Favored : 83.39 % 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: 1.99 (0.35), residues: 618 helix: 1.99 (0.28), residues: 342 sheet: 2.85 (1.23), residues: 14 loop : 0.44 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.599 Fit side-chains REVERT: I 77 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6945 (mmp80) REVERT: I 229 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: J 227 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6768 (tt0) outliers start: 12 outliers final: 6 residues processed: 100 average time/residue: 1.5802 time to fit residues: 163.4778 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.0303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5235 Z= 0.175 Angle : 0.539 6.495 7085 Z= 0.267 Chirality : 0.039 0.133 777 Planarity : 0.004 0.035 904 Dihedral : 8.319 134.235 702 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 15.88 % Favored : 82.67 % 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 (0.35), residues: 618 helix: 2.00 (0.28), residues: 343 sheet: 2.28 (1.29), residues: 15 loop : 0.54 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.015 0.001 TYR I 91 ARG 0.005 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.602 Fit side-chains REVERT: I 77 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6918 (mmp80) outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 1.5914 time to fit residues: 167.9209 Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5235 Z= 0.153 Angle : 0.515 6.664 7085 Z= 0.257 Chirality : 0.039 0.133 777 Planarity : 0.004 0.037 904 Dihedral : 8.179 132.693 701 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 16.06 % Favored : 82.49 % 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: 2.13 (0.35), residues: 618 helix: 2.12 (0.29), residues: 341 sheet: 3.06 (1.26), residues: 14 loop : 0.46 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.023 0.002 PHE I 125 TYR 0.015 0.001 TYR I 60 ARG 0.006 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.584 Fit side-chains REVERT: I 77 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6925 (mmp80) outliers start: 8 outliers final: 4 residues processed: 99 average time/residue: 1.5392 time to fit residues: 157.6361 Evaluate side-chains 97 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain J residue 292 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5235 Z= 0.149 Angle : 0.507 7.111 7085 Z= 0.252 Chirality : 0.039 0.133 777 Planarity : 0.004 0.038 904 Dihedral : 8.099 131.898 700 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 16.25 % Favored : 82.67 % 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: 2.19 (0.35), residues: 618 helix: 2.18 (0.29), residues: 341 sheet: 3.11 (1.25), residues: 14 loop : 0.48 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.003 0.001 HIS J 131 PHE 0.018 0.001 PHE I 125 TYR 0.015 0.001 TYR I 60 ARG 0.006 0.000 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.629 Fit side-chains REVERT: I 77 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6912 (mmp80) outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 1.4907 time to fit residues: 151.4815 Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 292 MET Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.210 Angle : 0.582 7.444 7085 Z= 0.289 Chirality : 0.041 0.135 777 Planarity : 0.004 0.034 904 Dihedral : 8.245 136.022 700 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 16.25 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.35), residues: 618 helix: 1.97 (0.28), residues: 340 sheet: 2.18 (1.25), residues: 15 loop : 0.39 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.025 0.002 PHE I 125 TYR 0.017 0.002 TYR I 91 ARG 0.007 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.574 Fit side-chains REVERT: I 77 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6938 (mmp80) outliers start: 9 outliers final: 2 residues processed: 100 average time/residue: 1.5167 time to fit residues: 156.8639 Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 136 GLN I 142 GLN I 155 ASN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5235 Z= 0.320 Angle : 0.698 8.657 7085 Z= 0.346 Chirality : 0.045 0.147 777 Planarity : 0.005 0.045 904 Dihedral : 8.412 140.060 700 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.62 % Allowed : 16.61 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.34), residues: 618 helix: 1.49 (0.27), residues: 341 sheet: 1.96 (1.24), residues: 15 loop : 0.21 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.022 0.003 PHE I 30 TYR 0.022 0.003 TYR I 2 ARG 0.012 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.631 Fit side-chains REVERT: I 63 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7204 (mmm160) REVERT: I 77 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6909 (mmp80) REVERT: I 229 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6583 (pm20) outliers start: 9 outliers final: 3 residues processed: 101 average time/residue: 1.6175 time to fit residues: 168.8352 Evaluate side-chains 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain J residue 228 THR Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN I 18 GLN I 136 GLN I 142 GLN I 275 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.186 Angle : 0.582 8.196 7085 Z= 0.287 Chirality : 0.040 0.139 777 Planarity : 0.004 0.035 904 Dihedral : 8.219 135.670 700 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 17.69 % Favored : 81.23 % 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 (0.34), residues: 618 helix: 1.85 (0.28), residues: 340 sheet: 2.15 (1.25), residues: 15 loop : 0.23 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.019 0.002 PHE I 125 TYR 0.015 0.002 TYR I 60 ARG 0.006 0.001 ARG I 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.628 Fit side-chains REVERT: I 77 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6921 (mmp80) outliers start: 6 outliers final: 2 residues processed: 99 average time/residue: 1.5693 time to fit residues: 160.7243 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain J residue 302 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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: 57.4502 > 50: distance: 44 - 211: 9.528 distance: 47 - 208: 5.318 distance: 53 - 196: 4.243 distance: 56 - 193: 6.272 distance: 113 - 204: 9.196 distance: 148 - 156: 8.809 distance: 156 - 157: 5.610 distance: 157 - 158: 10.509 distance: 157 - 160: 8.376 distance: 158 - 159: 17.413 distance: 158 - 165: 25.410 distance: 160 - 161: 6.693 distance: 162 - 163: 15.175 distance: 163 - 164: 10.079 distance: 165 - 166: 13.988 distance: 166 - 167: 20.856 distance: 166 - 169: 19.337 distance: 167 - 168: 24.052 distance: 167 - 171: 8.250 distance: 169 - 170: 8.964 distance: 171 - 172: 8.929 distance: 172 - 173: 17.510 distance: 172 - 175: 9.788 distance: 173 - 174: 21.203 distance: 173 - 179: 11.499 distance: 175 - 176: 6.802 distance: 176 - 177: 8.177 distance: 176 - 178: 13.966 distance: 179 - 180: 3.983 distance: 180 - 181: 5.627 distance: 181 - 182: 3.272 distance: 181 - 187: 4.616 distance: 183 - 184: 6.232 distance: 183 - 185: 5.670 distance: 184 - 186: 3.562 distance: 188 - 189: 6.440 distance: 188 - 191: 9.124 distance: 189 - 190: 6.974 distance: 191 - 192: 6.418 distance: 193 - 194: 8.569 distance: 194 - 197: 3.908 distance: 195 - 196: 6.644 distance: 197 - 198: 5.770 distance: 198 - 199: 8.050 distance: 198 - 200: 10.008 distance: 201 - 202: 5.689 distance: 202 - 205: 4.790 distance: 203 - 204: 5.830 distance: 203 - 208: 5.835 distance: 205 - 206: 6.832 distance: 205 - 207: 8.913 distance: 210 - 211: 7.377 distance: 210 - 219: 4.593 distance: 213 - 214: 3.043 distance: 220 - 221: 5.600 distance: 220 - 223: 3.828 distance: 221 - 222: 3.939 distance: 223 - 224: 3.277 distance: 224 - 226: 3.077 distance: 227 - 228: 3.869 distance: 228 - 229: 6.484 distance: 229 - 230: 6.173 distance: 229 - 238: 3.875 distance: 232 - 233: 3.794 distance: 233 - 235: 3.983 distance: 235 - 237: 4.354