Starting phenix.real_space_refine on Sun Aug 4 13:20:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/08_2024/7nkq_12446.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/08_2024/7nkq_12446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/08_2024/7nkq_12446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/08_2024/7nkq_12446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/08_2024/7nkq_12446.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/08_2024/7nkq_12446.cif" } resolution = 2.98 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: 5 Type Number sf(0) Gaussians S 7 5.16 5 C 3278 2.51 5 N 946 2.21 5 O 1078 1.98 5 H 5312 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 81": "OD1" <-> "OD2" 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: 10621 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1500 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 917 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain breaks: 3 Chain: "C" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 643 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain breaks: 3 Chain: "D" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 752 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 4 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 721 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain breaks: 2 Chain: "F" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 559 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 3 Chain: "d" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5002 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 10, 'TRANS': 319} Chain breaks: 1 Chain: "b" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 527 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 6.93, per 1000 atoms: 0.65 Number of scatterers: 10621 At special positions: 0 Unit cell: (112.05, 77.19, 83.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 1078 8.00 N 946 7.00 C 3278 6.00 H 5312 1.00 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: 9.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 41.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 4.189A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'B' and resid 9 through 21 removed outlier: 3.745A pdb=" N ILE B 15 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'd' and resid 110 through 137 Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 190 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 222 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.876A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 313 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 371 Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 Processing helix chain 'b' and resid 131 through 160 removed outlier: 3.611A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 591 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: 3.32 Time building geometry restraints manager: 9.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5310 1.03 - 1.23: 6 1.23 - 1.42: 2098 1.42 - 1.61: 3226 1.61 - 1.81: 12 Bond restraints: 10652 Sorted by residual: bond pdb=" CA ARG E 63 " pdb=" CB ARG E 63 " ideal model delta sigma weight residual 1.528 1.502 0.027 2.61e-02 1.47e+03 1.05e+00 bond pdb=" CG GLU d 155 " pdb=" CD GLU d 155 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.23e-01 bond pdb=" CB ARG E 14 " pdb=" CG ARG E 14 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.20e-01 bond pdb=" CB ASP A 70 " pdb=" CG ASP A 70 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 bond pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.86e-01 ... (remaining 10647 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.20: 216 107.20 - 113.88: 13258 113.88 - 120.56: 3160 120.56 - 127.25: 2608 127.25 - 133.93: 40 Bond angle restraints: 19282 Sorted by residual: angle pdb=" N GLU d 155 " pdb=" CA GLU d 155 " pdb=" CB GLU d 155 " ideal model delta sigma weight residual 110.12 114.15 -4.03 1.47e+00 4.63e-01 7.51e+00 angle pdb=" N GLU d 205 " pdb=" CA GLU d 205 " pdb=" CB GLU d 205 " ideal model delta sigma weight residual 110.12 113.26 -3.14 1.47e+00 4.63e-01 4.56e+00 angle pdb=" C LEU d 154 " pdb=" N GLU d 155 " pdb=" CA GLU d 155 " ideal model delta sigma weight residual 120.28 117.83 2.45 1.34e+00 5.57e-01 3.36e+00 angle pdb=" CA GLN d 112 " pdb=" CB GLN d 112 " pdb=" CG GLN d 112 " ideal model delta sigma weight residual 114.10 117.74 -3.64 2.00e+00 2.50e-01 3.32e+00 angle pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " pdb=" CD GLU C 16 " ideal model delta sigma weight residual 112.60 115.61 -3.01 1.70e+00 3.46e-01 3.14e+00 ... (remaining 19277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4359 16.36 - 32.72: 406 32.72 - 49.08: 95 49.08 - 65.44: 44 65.44 - 81.80: 7 Dihedral angle restraints: 4911 sinusoidal: 2783 harmonic: 2128 Sorted by residual: dihedral pdb=" CA LEU d 409 " pdb=" C LEU d 409 " pdb=" N HIS d 410 " pdb=" CA HIS d 410 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP d 197 " pdb=" CB ASP d 197 " pdb=" CG ASP d 197 " pdb=" OD1 ASP d 197 " ideal model delta sinusoidal sigma weight residual -30.00 -88.29 58.29 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP b 163 " pdb=" CB ASP b 163 " pdb=" CG ASP b 163 " pdb=" OD1 ASP b 163 " ideal model delta sinusoidal sigma weight residual -30.00 -86.06 56.06 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 559 0.027 - 0.054: 197 0.054 - 0.082: 63 0.082 - 0.109: 45 0.109 - 0.136: 28 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA VAL B 74 " pdb=" N VAL B 74 " pdb=" C VAL B 74 " pdb=" CB VAL B 74 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA GLU C 16 " pdb=" N GLU C 16 " pdb=" C GLU C 16 " pdb=" CB GLU C 16 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE d 428 " pdb=" N ILE d 428 " pdb=" C ILE d 428 " pdb=" CB ILE d 428 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 889 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP d 269 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASP d 269 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP d 269 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA d 270 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN d 112 " -0.006 2.00e-02 2.50e+03 1.07e-02 1.70e+00 pdb=" CD GLN d 112 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN d 112 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN d 112 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN d 112 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN d 112 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA d 275 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C ALA d 275 " 0.022 2.00e-02 2.50e+03 pdb=" O ALA d 275 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG d 276 " -0.007 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 583 2.18 - 2.79: 22145 2.79 - 3.39: 30036 3.39 - 4.00: 38130 4.00 - 4.60: 58562 Nonbonded interactions: 149456 Sorted by model distance: nonbonded pdb=" O SER A 20 " pdb="HH12 ARG b 158 " model vdw 1.575 2.450 nonbonded pdb=" O ASN B 68 " pdb=" H GLY B 75 " model vdw 1.602 2.450 nonbonded pdb=" H ALA D 54 " pdb=" O ARG D 63 " model vdw 1.604 2.450 nonbonded pdb=" HH TYR d 401 " pdb=" OE1 GLU d 426 " model vdw 1.605 2.450 nonbonded pdb=" O GLU d 225 " pdb=" HZ1 LYS d 233 " model vdw 1.611 2.450 ... (remaining 149451 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=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: 7.170 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: 0.190 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 40.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.004 0.029 5340 Z= 0.274 Angle : 0.490 4.141 7215 Z= 0.264 Chirality : 0.041 0.136 892 Planarity : 0.003 0.033 945 Dihedral : 13.517 81.800 1951 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 662 helix: 1.88 (0.30), residues: 311 sheet: -0.90 (0.53), residues: 85 loop : 0.56 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.010 0.001 PHE d 150 TYR 0.011 0.002 TYR C 18 ARG 0.007 0.000 ARG d 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7632 (t0) cc_final: 0.7398 (t0) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 2.5907 time to fit residues: 200.0727 Evaluate side-chains 51 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5340 Z= 0.223 Angle : 0.484 5.008 7215 Z= 0.255 Chirality : 0.040 0.135 892 Planarity : 0.004 0.046 945 Dihedral : 3.750 18.175 745 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.35 % Allowed : 8.54 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.34), residues: 662 helix: 2.26 (0.30), residues: 311 sheet: -1.32 (0.55), residues: 76 loop : 0.66 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS d 410 PHE 0.009 0.001 PHE d 187 TYR 0.010 0.002 TYR C 18 ARG 0.009 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7674 (t0) cc_final: 0.7292 (t0) REVERT: F 78 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7310 (mp0) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 1.9501 time to fit residues: 113.9549 Evaluate side-chains 51 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5340 Z= 0.346 Angle : 0.497 5.125 7215 Z= 0.262 Chirality : 0.041 0.131 892 Planarity : 0.004 0.068 945 Dihedral : 3.777 18.635 743 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.17 % Allowed : 9.76 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.34), residues: 662 helix: 2.24 (0.29), residues: 312 sheet: -1.47 (0.55), residues: 76 loop : 0.54 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.004 0.001 HIS A 43 PHE 0.010 0.001 PHE d 187 TYR 0.009 0.002 TYR C 18 ARG 0.008 0.000 ARG d 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7665 (t0) cc_final: 0.7260 (t0) REVERT: F 78 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7349 (mp0) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 1.8967 time to fit residues: 102.9412 Evaluate side-chains 48 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.0470 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5340 Z= 0.210 Angle : 0.458 4.989 7215 Z= 0.238 Chirality : 0.040 0.130 892 Planarity : 0.004 0.067 945 Dihedral : 3.606 17.727 743 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.05 % Allowed : 10.10 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.35), residues: 662 helix: 2.42 (0.29), residues: 312 sheet: -1.57 (0.55), residues: 76 loop : 0.59 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.002 0.001 HIS d 410 PHE 0.008 0.001 PHE d 150 TYR 0.008 0.002 TYR B 18 ARG 0.009 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7573 (t0) cc_final: 0.7162 (t0) REVERT: F 78 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 2.0857 time to fit residues: 120.0686 Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5340 Z= 0.239 Angle : 0.467 5.089 7215 Z= 0.242 Chirality : 0.040 0.129 892 Planarity : 0.004 0.071 945 Dihedral : 3.578 17.526 743 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 11.50 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.35), residues: 662 helix: 2.46 (0.29), residues: 312 sheet: -1.60 (0.55), residues: 76 loop : 0.57 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.009 0.001 PHE d 150 TYR 0.007 0.002 TYR B 18 ARG 0.010 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7563 (t0) cc_final: 0.7140 (t0) REVERT: F 78 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7346 (mp0) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 1.9853 time to fit residues: 109.6538 Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5340 Z= 0.247 Angle : 0.470 5.649 7215 Z= 0.244 Chirality : 0.040 0.129 892 Planarity : 0.004 0.080 945 Dihedral : 3.566 17.334 743 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.22 % Allowed : 12.02 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.35), residues: 662 helix: 2.51 (0.29), residues: 312 sheet: -1.57 (0.56), residues: 76 loop : 0.56 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS A 43 PHE 0.009 0.001 PHE d 150 TYR 0.007 0.001 TYR B 18 ARG 0.012 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7557 (t0) cc_final: 0.7116 (t0) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 2.0749 time to fit residues: 116.3758 Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5340 Z= 0.353 Angle : 0.515 6.195 7215 Z= 0.269 Chirality : 0.041 0.128 892 Planarity : 0.004 0.084 945 Dihedral : 3.723 18.114 743 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.05 % Allowed : 13.41 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.34), residues: 662 helix: 2.39 (0.29), residues: 312 sheet: -1.68 (0.56), residues: 76 loop : 0.44 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP d 261 HIS 0.004 0.001 HIS A 43 PHE 0.010 0.001 PHE d 187 TYR 0.007 0.002 TYR d 316 ARG 0.012 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7581 (t0) cc_final: 0.7135 (t0) REVERT: F 78 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7342 (mp0) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 2.1032 time to fit residues: 113.3538 Evaluate side-chains 51 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5340 Z= 0.209 Angle : 0.476 5.172 7215 Z= 0.247 Chirality : 0.040 0.130 892 Planarity : 0.004 0.086 945 Dihedral : 3.597 17.659 743 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.05 % Allowed : 13.76 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.35), residues: 662 helix: 2.58 (0.29), residues: 312 sheet: -1.71 (0.56), residues: 76 loop : 0.52 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.001 HIS E 56 PHE 0.008 0.001 PHE d 150 TYR 0.006 0.001 TYR B 18 ARG 0.011 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7540 (t0) cc_final: 0.7104 (t0) REVERT: F 78 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7344 (mp0) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 2.0933 time to fit residues: 113.0715 Evaluate side-chains 53 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.0270 chunk 55 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5340 Z= 0.204 Angle : 0.478 8.044 7215 Z= 0.246 Chirality : 0.040 0.128 892 Planarity : 0.004 0.086 945 Dihedral : 3.511 17.375 743 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.05 % Allowed : 14.11 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.35), residues: 662 helix: 2.63 (0.29), residues: 312 sheet: -1.71 (0.56), residues: 76 loop : 0.53 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.000 HIS A 43 PHE 0.008 0.001 PHE d 150 TYR 0.006 0.001 TYR B 18 ARG 0.013 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7534 (t0) cc_final: 0.7073 (t0) REVERT: F 78 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7353 (mp0) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 2.1141 time to fit residues: 109.7225 Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5340 Z= 0.235 Angle : 0.488 7.487 7215 Z= 0.252 Chirality : 0.040 0.129 892 Planarity : 0.004 0.086 945 Dihedral : 3.527 17.361 743 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 14.11 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.35), residues: 662 helix: 2.65 (0.29), residues: 312 sheet: -1.69 (0.56), residues: 76 loop : 0.51 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.003 0.001 HIS A 43 PHE 0.008 0.001 PHE d 187 TYR 0.006 0.001 TYR d 316 ARG 0.011 0.000 ARG E 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7539 (t0) cc_final: 0.7080 (t0) REVERT: F 78 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7357 (mp0) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 2.1192 time to fit residues: 109.9039 Evaluate side-chains 51 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain d residue 423 VAL 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: 69.1811 > 50: distance: 275 - 286: 28.517 distance: 286 - 287: 34.446 distance: 286 - 292: 34.188 distance: 287 - 288: 20.225 distance: 287 - 290: 27.608 distance: 287 - 293: 24.119 distance: 288 - 289: 45.679 distance: 288 - 300: 46.914 distance: 290 - 291: 41.692 distance: 290 - 294: 55.096 distance: 290 - 295: 31.345 distance: 291 - 292: 11.677 distance: 291 - 296: 41.465 distance: 291 - 297: 38.479 distance: 292 - 298: 45.334 distance: 292 - 299: 55.409 distance: 300 - 301: 49.409 distance: 300 - 307: 41.623 distance: 301 - 302: 17.938 distance: 301 - 304: 28.407 distance: 301 - 308: 22.121 distance: 302 - 303: 38.771 distance: 302 - 316: 38.801 distance: 304 - 305: 25.103 distance: 304 - 306: 42.529 distance: 304 - 309: 33.235 distance: 305 - 310: 13.983 distance: 305 - 311: 17.940 distance: 305 - 312: 40.798 distance: 306 - 313: 46.225 distance: 306 - 314: 35.662 distance: 306 - 315: 24.670 distance: 316 - 317: 56.355 distance: 316 - 322: 43.468 distance: 317 - 318: 50.512 distance: 317 - 320: 35.520 distance: 317 - 323: 51.137 distance: 318 - 319: 17.783 distance: 318 - 327: 47.241 distance: 320 - 321: 38.276 distance: 320 - 324: 35.073 distance: 320 - 325: 50.227 distance: 321 - 326: 37.313 distance: 327 - 328: 21.919 distance: 327 - 334: 36.619 distance: 328 - 329: 22.450 distance: 328 - 331: 23.127 distance: 328 - 335: 25.937 distance: 329 - 330: 52.045 distance: 329 - 343: 16.679 distance: 331 - 332: 28.124 distance: 331 - 333: 24.428 distance: 331 - 336: 18.511 distance: 332 - 337: 18.805 distance: 332 - 338: 20.323 distance: 332 - 339: 23.164 distance: 333 - 340: 38.526 distance: 333 - 341: 43.840 distance: 333 - 342: 21.501 distance: 343 - 344: 29.617 distance: 343 - 352: 42.321 distance: 344 - 345: 49.456 distance: 344 - 347: 46.850 distance: 344 - 353: 10.897 distance: 345 - 346: 43.391 distance: 345 - 360: 41.742 distance: 347 - 348: 44.262 distance: 347 - 354: 50.024 distance: 347 - 355: 39.970 distance: 348 - 349: 27.049 distance: 348 - 356: 43.083 distance: 348 - 357: 41.194 distance: 349 - 350: 12.748 distance: 349 - 351: 11.836 distance: 351 - 358: 29.247 distance: 351 - 359: 16.139 distance: 360 - 361: 31.144 distance: 360 - 368: 37.400 distance: 361 - 362: 29.589 distance: 361 - 364: 33.417 distance: 361 - 369: 30.484 distance: 362 - 363: 32.938 distance: 362 - 379: 13.997 distance: 364 - 365: 31.239 distance: 364 - 370: 32.983 distance: 364 - 371: 26.932 distance: 365 - 366: 6.612 distance: 365 - 367: 27.417 distance: 365 - 372: 17.503 distance: 366 - 373: 22.216 distance: 366 - 374: 16.498 distance: 366 - 375: 6.050 distance: 367 - 376: 24.402 distance: 367 - 377: 26.487 distance: 367 - 378: 26.146 distance: 379 - 380: 50.580 distance: 379 - 389: 35.672 distance: 380 - 381: 30.076 distance: 380 - 383: 35.296 distance: 380 - 390: 54.789 distance: 381 - 382: 30.723 distance: 381 - 396: 26.396 distance: 383 - 384: 8.342 distance: 383 - 391: 25.273 distance: 383 - 392: 23.514 distance: 384 - 385: 13.446 distance: 384 - 386: 10.187 distance: 385 - 387: 12.884 distance: 386 - 388: 10.736 distance: 386 - 393: 6.065 distance: 387 - 388: 17.606 distance: 387 - 394: 16.983 distance: 396 - 397: 34.779 distance: 396 - 403: 22.703 distance: 397 - 398: 14.382 distance: 397 - 400: 46.232 distance: 397 - 404: 33.444 distance: 398 - 399: 16.703 distance: 398 - 412: 31.534 distance: 400 - 401: 35.165 distance: 400 - 402: 22.433 distance: 400 - 405: 18.291 distance: 401 - 406: 27.052 distance: 401 - 407: 13.109 distance: 401 - 408: 16.684 distance: 402 - 409: 9.794 distance: 402 - 410: 30.886 distance: 402 - 411: 36.688 distance: 412 - 413: 47.500 distance: 412 - 420: 40.060 distance: 413 - 414: 32.485 distance: 413 - 416: 14.569 distance: 413 - 421: 43.371 distance: 414 - 415: 54.945 distance: 414 - 424: 55.735 distance: 416 - 417: 22.048 distance: 416 - 422: 57.871 distance: 416 - 423: 61.806 distance: 417 - 418: 47.346 distance: 417 - 419: 44.785 distance: 424 - 425: 29.825 distance: 424 - 430: 48.222 distance: 425 - 426: 21.359 distance: 425 - 428: 20.836 distance: 425 - 431: 55.272 distance: 426 - 427: 27.808 distance: 426 - 438: 16.471 distance: 428 - 429: 25.764 distance: 428 - 432: 21.850 distance: 428 - 433: 16.671 distance: 429 - 430: 42.990 distance: 429 - 434: 43.018 distance: 429 - 435: 34.738 distance: 430 - 436: 10.620 distance: 430 - 437: 22.341