Starting phenix.real_space_refine on Fri Jan 19 06:17:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/01_2024/7nkq_12446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/01_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_12446/01_2024/7nkq_12446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/01_2024/7nkq_12446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/01_2024/7nkq_12446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkq_12446/01_2024/7nkq_12446.pdb" } 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-1.21-5211/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: 5.09, per 1000 atoms: 0.48 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: 8.22 Conformation dependent library (CDL) restraints added in 1.0 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: 3.20 Time building geometry restraints manager: 8.48 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: 4333 16.36 - 32.72: 372 32.72 - 49.08: 65 49.08 - 65.44: 11 65.44 - 81.80: 7 Dihedral angle restraints: 4788 sinusoidal: 2660 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 4785 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 1.850 nonbonded pdb=" O ASN B 68 " pdb=" H GLY B 75 " model vdw 1.602 1.850 nonbonded pdb=" H ALA D 54 " pdb=" O ARG D 63 " model vdw 1.604 1.850 nonbonded pdb=" HH TYR d 401 " pdb=" OE1 GLU d 426 " model vdw 1.605 1.850 nonbonded pdb=" O GLU d 225 " pdb=" HZ1 LYS d 233 " model vdw 1.611 1.850 ... (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 ========== 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: 5.650 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: 0.180 Extract box with map and model: 24.470 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.250 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.760 ------------------------------------------------------------------------------- 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 : 0.879 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: 2.6742 time to fit residues: 206.7212 Evaluate side-chains 51 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5340 Z= 0.206 Angle : 0.460 5.356 7215 Z= 0.239 Chirality : 0.040 0.126 892 Planarity : 0.004 0.055 945 Dihedral : 3.705 22.136 745 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.87 % Allowed : 7.84 % Favored : 91.29 % 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: 1.91 (0.35), residues: 662 helix: 2.34 (0.30), residues: 311 sheet: -0.80 (0.62), residues: 71 loop : 0.75 (0.41), residues: 280 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 0.007 0.001 PHE d 150 TYR 0.010 0.002 TYR C 18 ARG 0.010 0.000 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 62 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7605 (t0) cc_final: 0.7250 (t0) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 1.8664 time to fit residues: 121.1708 Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain C residue 70 ASP 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: 0.0770 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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: 0.8065 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5340 Z= 0.178 Angle : 0.430 4.080 7215 Z= 0.222 Chirality : 0.039 0.127 892 Planarity : 0.004 0.068 945 Dihedral : 3.533 21.686 745 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.87 % Allowed : 8.89 % Favored : 90.24 % 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: 2.09 (0.35), residues: 662 helix: 2.58 (0.30), residues: 311 sheet: -0.76 (0.63), residues: 71 loop : 0.73 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.000 HIS d 410 PHE 0.007 0.001 PHE d 150 TYR 0.008 0.001 TYR C 18 ARG 0.008 0.000 ARG E 26 *********************** 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 56 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7603 (t0) cc_final: 0.7298 (t0) outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 1.8762 time to fit residues: 111.8673 Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5340 Z= 0.326 Angle : 0.470 4.171 7215 Z= 0.246 Chirality : 0.041 0.124 892 Planarity : 0.004 0.070 945 Dihedral : 3.710 24.686 745 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.22 % Allowed : 10.10 % Favored : 88.68 % 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: 1.91 (0.34), residues: 662 helix: 2.45 (0.30), residues: 311 sheet: -0.79 (0.60), residues: 76 loop : 0.62 (0.41), residues: 275 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 150 TYR 0.008 0.002 TYR d 316 ARG 0.010 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: 7 poor density : 50 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7613 (t0) cc_final: 0.7297 (t0) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 1.9073 time to fit residues: 111.4045 Evaluate side-chains 52 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 ASP 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: 0.9990 chunk 27 optimal weight: 0.0270 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 59 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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: 0.8078 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5340 Z= 0.208 Angle : 0.448 5.423 7215 Z= 0.230 Chirality : 0.039 0.126 892 Planarity : 0.004 0.073 945 Dihedral : 3.591 23.904 745 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.05 % Allowed : 10.98 % Favored : 87.98 % 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: 2.11 (0.35), residues: 662 helix: 2.63 (0.30), residues: 311 sheet: -0.71 (0.63), residues: 71 loop : 0.68 (0.41), residues: 280 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 0.008 0.001 PHE d 150 TYR 0.007 0.001 TYR d 316 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 58 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7607 (t0) cc_final: 0.7334 (t0) outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 1.8702 time to fit residues: 111.5795 Evaluate side-chains 56 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain E residue 80 THR 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: 4.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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: 0.8085 moved from start: 0.1002 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= 0.228 Angle : 0.447 5.154 7215 Z= 0.230 Chirality : 0.039 0.126 892 Planarity : 0.004 0.077 945 Dihedral : 3.546 23.976 745 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 11.15 % Favored : 87.80 % 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: 2.14 (0.35), residues: 662 helix: 2.66 (0.30), residues: 311 sheet: -0.74 (0.60), residues: 76 loop : 0.73 (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 A 43 PHE 0.008 0.001 PHE d 150 TYR 0.007 0.001 TYR d 316 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: 6 poor density : 51 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7592 (t0) cc_final: 0.7321 (t0) outliers start: 6 outliers final: 6 residues processed: 56 average time/residue: 1.8322 time to fit residues: 109.2771 Evaluate side-chains 56 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 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: 0.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.1058 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= 0.271 Angle : 0.462 5.351 7215 Z= 0.238 Chirality : 0.040 0.125 892 Planarity : 0.004 0.081 945 Dihedral : 3.603 24.749 745 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.39 % Allowed : 11.67 % Favored : 86.93 % 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: 2.10 (0.35), residues: 662 helix: 2.63 (0.30), residues: 311 sheet: -0.72 (0.60), residues: 76 loop : 0.70 (0.41), residues: 275 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 150 TYR 0.007 0.001 TYR d 316 ARG 0.011 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 59 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7601 (t0) cc_final: 0.7335 (t0) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 1.7783 time to fit residues: 108.4823 Evaluate side-chains 54 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.8080 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5340 Z= 0.205 Angle : 0.452 5.285 7215 Z= 0.233 Chirality : 0.040 0.126 892 Planarity : 0.004 0.084 945 Dihedral : 3.546 24.523 745 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.22 % Allowed : 12.54 % Favored : 86.24 % 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: 2.22 (0.35), residues: 662 helix: 2.73 (0.30), residues: 311 sheet: -0.66 (0.60), residues: 76 loop : 0.75 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP d 261 HIS 0.002 0.000 HIS d 410 PHE 0.008 0.001 PHE d 150 TYR 0.007 0.001 TYR d 316 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 57 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7599 (t0) cc_final: 0.7275 (t0) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 1.6840 time to fit residues: 98.9103 Evaluate side-chains 56 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.1116 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= 0.335 Angle : 0.489 5.489 7215 Z= 0.254 Chirality : 0.041 0.124 892 Planarity : 0.004 0.089 945 Dihedral : 3.736 26.615 745 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.05 % Allowed : 12.89 % Favored : 86.06 % 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: 1.99 (0.34), residues: 662 helix: 2.55 (0.30), residues: 311 sheet: -0.72 (0.60), residues: 76 loop : 0.60 (0.41), residues: 275 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 0.009 0.001 PHE d 150 TYR 0.009 0.002 TYR d 316 ARG 0.012 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 53 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7596 (t0) cc_final: 0.7305 (t0) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 1.8571 time to fit residues: 102.9589 Evaluate side-chains 53 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 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: 0.8092 moved from start: 0.1166 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= 0.246 Angle : 0.463 5.342 7215 Z= 0.239 Chirality : 0.040 0.125 892 Planarity : 0.004 0.092 945 Dihedral : 3.661 25.976 745 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 2.11 (0.35), residues: 662 helix: 2.66 (0.30), residues: 311 sheet: -0.65 (0.60), residues: 76 loop : 0.65 (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 0.008 0.001 PHE d 150 TYR 0.007 0.001 TYR d 316 ARG 0.012 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 54 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: C 68 ASN cc_start: 0.7599 (t0) cc_final: 0.7313 (t0) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 1.8454 time to fit residues: 104.2616 Evaluate side-chains 53 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain C residue 70 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.0170 chunk 9 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.102154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074039 restraints weight = 32111.885| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.00 r_work: 0.3078 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5340 Z= 0.184 Angle : 0.451 6.257 7215 Z= 0.232 Chirality : 0.039 0.126 892 Planarity : 0.004 0.089 945 Dihedral : 3.527 24.438 745 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.22 % Allowed : 13.07 % Favored : 85.71 % 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: 2.26 (0.35), residues: 662 helix: 2.80 (0.30), residues: 311 sheet: -0.64 (0.59), residues: 76 loop : 0.72 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP d 261 HIS 0.002 0.000 HIS d 410 PHE 0.007 0.001 PHE d 150 TYR 0.006 0.001 TYR d 316 ARG 0.011 0.000 ARG E 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4486.18 seconds wall clock time: 79 minutes 49.40 seconds (4789.40 seconds total)