Starting phenix.real_space_refine on Fri Feb 16 10:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnt_17784/02_2024/8pnt_17784_trim_updated.pdb" } resolution = 3.46 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= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 4854 2.51 5 N 1305 2.21 5 O 1403 1.98 5 H 7508 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15117 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 12251 Classifications: {'peptide': 749} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 708} Chain breaks: 2 Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2416 Classifications: {'peptide': 151} Link IDs: {'TRANS': 150} Chain: "C" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 306 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 111 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MGT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.81, per 1000 atoms: 0.45 Number of scatterers: 15117 At special positions: 0 Unit cell: (99.002, 92.29, 114.943, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 3 15.00 O 1403 8.00 N 1305 7.00 C 4854 6.00 H 7508 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: 13.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 1 sheets defined 62.7% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 80 through 96 removed outlier: 6.104A pdb=" N THR A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 89 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 93 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 94 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 118 Processing helix chain 'A' and resid 121 through 137 removed outlier: 3.765A pdb=" N ASN A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.935A pdb=" N THR A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 205 removed outlier: 3.668A pdb=" N PHE A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 6.636A pdb=" N LYS A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 228 through 241 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 257 through 260 No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 347 through 359 Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.730A pdb=" N THR A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 400 Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.921A pdb=" N ASP A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 471 through 476 removed outlier: 4.460A pdb=" N ALA A 475 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 510 Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 541 through 554 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 635 through 674 Processing helix chain 'A' and resid 684 through 731 Processing helix chain 'A' and resid 738 through 768 removed outlier: 5.584A pdb=" N GLN A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N THR A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.963A pdb=" N VAL A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 10 No H-bonds generated for 'chain 'B' and resid 7 through 10' Processing helix chain 'B' and resid 29 through 36 Processing helix chain 'B' and resid 53 through 62 removed outlier: 4.394A pdb=" N LYS B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'C' and resid 117 through 131 Processing sheet with id= A, first strand: chain 'B' and resid 112 through 116 removed outlier: 4.420A pdb=" N THR B 41 " --> pdb=" O ASP B 116 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1140 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: 5.49 Time building geometry restraints manager: 13.52 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: 7486 1.03 - 1.23: 22 1.23 - 1.42: 3294 1.42 - 1.62: 4427 1.62 - 1.81: 66 Bond restraints: 15295 Sorted by residual: bond pdb=" C3' MGT B 201 " pdb=" C4' MGT B 201 " ideal model delta sigma weight residual 1.265 1.537 -0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C1' MGT B 201 " pdb=" C2' MGT B 201 " ideal model delta sigma weight residual 1.263 1.524 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C2 MGT B 201 " pdb=" N3 MGT B 201 " ideal model delta sigma weight residual 1.481 1.320 0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C4 MGT B 201 " pdb=" N3 MGT B 201 " ideal model delta sigma weight residual 1.484 1.346 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C2' MGT B 201 " pdb=" C3' MGT B 201 " ideal model delta sigma weight residual 1.652 1.514 0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 15290 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.14: 343 107.14 - 113.85: 17985 113.85 - 120.57: 5369 120.57 - 127.28: 3831 127.28 - 134.00: 104 Bond angle restraints: 27632 Sorted by residual: angle pdb=" CA ILE B 111 " pdb=" C ILE B 111 " pdb=" O ILE B 111 " ideal model delta sigma weight residual 121.59 118.00 3.59 1.03e+00 9.43e-01 1.22e+01 angle pdb=" O1B MGT B 201 " pdb=" PB MGT B 201 " pdb=" O2B MGT B 201 " ideal model delta sigma weight residual 109.56 119.64 -10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA ILE B 110 " pdb=" C ILE B 110 " pdb=" O ILE B 110 " ideal model delta sigma weight residual 120.78 116.93 3.85 1.25e+00 6.40e-01 9.50e+00 angle pdb=" C5 MGT B 201 " pdb=" C6 MGT B 201 " pdb=" N1 MGT B 201 " ideal model delta sigma weight residual 119.62 110.55 9.07 3.00e+00 1.11e-01 9.14e+00 angle pdb=" O1A MGT B 201 " pdb=" PA MGT B 201 " pdb=" O2A MGT B 201 " ideal model delta sigma weight residual 109.47 118.38 -8.91 3.00e+00 1.11e-01 8.83e+00 ... (remaining 27627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6628 17.69 - 35.38: 405 35.38 - 53.07: 107 53.07 - 70.76: 33 70.76 - 88.45: 7 Dihedral angle restraints: 7180 sinusoidal: 3887 harmonic: 3293 Sorted by residual: dihedral pdb=" CA GLN A 245 " pdb=" C GLN A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LYS A 37 " pdb=" C LYS A 37 " pdb=" N VAL A 38 " pdb=" CA VAL A 38 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG B 146 " pdb=" CD ARG B 146 " pdb=" NE ARG B 146 " pdb=" CZ ARG B 146 " ideal model delta sinusoidal sigma weight residual 180.00 136.27 43.73 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 7177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 994 0.050 - 0.100: 124 0.100 - 0.149: 27 0.149 - 0.199: 3 0.199 - 0.249: 1 Chirality restraints: 1149 Sorted by residual: chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2' MGT B 201 " pdb=" C1' MGT B 201 " pdb=" C3' MGT B 201 " pdb=" O2' MGT B 201 " both_signs ideal model delta sigma weight residual False -2.45 -2.62 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ARG B 112 " pdb=" N ARG B 112 " pdb=" C ARG B 112 " pdb=" CB ARG B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 1146 not shown) Planarity restraints: 2228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 73 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C CYS A 73 " 0.046 2.00e-02 2.50e+03 pdb=" O CYS A 73 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 120 " 0.012 2.00e-02 2.50e+03 1.96e-02 5.75e+00 pdb=" CG ASN A 120 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 120 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 120 " 0.033 2.00e-02 2.50e+03 pdb="HD21 ASN A 120 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 120 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 185 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C TYR A 185 " -0.034 2.00e-02 2.50e+03 pdb=" O TYR A 185 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU A 186 " 0.011 2.00e-02 2.50e+03 ... (remaining 2225 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 573 2.17 - 2.78: 29796 2.78 - 3.38: 42770 3.38 - 3.99: 53502 3.99 - 4.60: 86223 Nonbonded interactions: 212864 Sorted by model distance: nonbonded pdb=" OE1 GLU A 246 " pdb=" H ILE A 249 " model vdw 1.560 1.850 nonbonded pdb=" O THR A 277 " pdb=" HG SER A 280 " model vdw 1.560 1.850 nonbonded pdb=" O GLU A 158 " pdb="HH21 ARG A 166 " model vdw 1.568 1.850 nonbonded pdb="HD21 ASN A 136 " pdb=" O TRP A 179 " model vdw 1.597 1.850 nonbonded pdb=" O VAL A 139 " pdb=" H HIS A 266 " model vdw 1.619 1.850 ... (remaining 212859 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: 1.110 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: 0.200 Extract box with map and model: 4.210 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 52.280 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.007 0.272 7787 Z= 0.403 Angle : 0.582 10.078 10542 Z= 0.292 Chirality : 0.037 0.249 1149 Planarity : 0.004 0.039 1348 Dihedral : 13.553 88.452 2913 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.84 % Favored : 96.94 % Rotamer: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.52 (0.29), residues: 915 helix: 1.61 (0.22), residues: 569 sheet: -2.10 (1.17), residues: 16 loop : 0.24 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 638 HIS 0.006 0.001 HIS D 389 PHE 0.013 0.001 PHE A 417 TYR 0.009 0.001 TYR A 228 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.9188 (ttm) cc_final: 0.8674 (ttp) REVERT: A 242 ASP cc_start: 0.8954 (m-30) cc_final: 0.8653 (t0) REVERT: A 371 MET cc_start: 0.9435 (tmm) cc_final: 0.9170 (tmm) REVERT: A 400 MET cc_start: 0.9356 (mmm) cc_final: 0.9123 (mmm) REVERT: A 432 ASP cc_start: 0.9043 (m-30) cc_final: 0.8716 (m-30) REVERT: A 635 LEU cc_start: 0.8265 (tp) cc_final: 0.7975 (tp) REVERT: B 38 LYS cc_start: 0.9441 (pttt) cc_final: 0.9197 (tptp) REVERT: B 54 GLU cc_start: 0.8948 (mp0) cc_final: 0.8570 (mp0) outliers start: 1 outliers final: 1 residues processed: 161 average time/residue: 0.6484 time to fit residues: 129.0488 Evaluate side-chains 71 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7787 Z= 0.276 Angle : 0.512 5.020 10542 Z= 0.270 Chirality : 0.035 0.136 1149 Planarity : 0.004 0.043 1348 Dihedral : 4.462 55.614 1018 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.08 % Allowed : 10.53 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.23 (0.28), residues: 915 helix: 2.20 (0.22), residues: 570 sheet: -1.51 (1.26), residues: 16 loop : 0.45 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 638 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 569 TYR 0.011 0.001 TYR A 228 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ASP cc_start: 0.9067 (m-30) cc_final: 0.8691 (t0) REVERT: A 250 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8875 (mp) REVERT: A 371 MET cc_start: 0.9493 (tmm) cc_final: 0.9259 (tmm) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.5612 time to fit residues: 58.5697 Evaluate side-chains 68 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.8620 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7787 Z= 0.229 Angle : 0.501 7.797 10542 Z= 0.261 Chirality : 0.035 0.126 1149 Planarity : 0.004 0.033 1348 Dihedral : 4.359 52.422 1018 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.67 % Allowed : 11.12 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.53 (0.28), residues: 915 helix: 2.40 (0.22), residues: 577 sheet: -1.28 (1.27), residues: 16 loop : 0.59 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 638 HIS 0.004 0.001 HIS A 498 PHE 0.014 0.001 PHE A 292 TYR 0.008 0.001 TYR A 228 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8147 (tptp) cc_final: 0.7934 (tptp) REVERT: A 242 ASP cc_start: 0.9107 (m-30) cc_final: 0.8720 (t0) REVERT: A 250 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8886 (mp) REVERT: A 371 MET cc_start: 0.9509 (tmm) cc_final: 0.9300 (tmm) outliers start: 14 outliers final: 8 residues processed: 74 average time/residue: 0.5524 time to fit residues: 54.2966 Evaluate side-chains 71 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.8645 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7787 Z= 0.231 Angle : 0.482 5.830 10542 Z= 0.253 Chirality : 0.034 0.124 1149 Planarity : 0.003 0.031 1348 Dihedral : 4.387 50.148 1018 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.67 % Allowed : 10.05 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.87 (0.28), residues: 915 helix: 2.68 (0.21), residues: 571 sheet: -1.01 (1.32), residues: 16 loop : 0.73 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 638 HIS 0.004 0.001 HIS A 498 PHE 0.020 0.001 PHE A 292 TYR 0.009 0.001 TYR A 228 ARG 0.003 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8245 (tptp) cc_final: 0.8028 (tptp) REVERT: A 242 ASP cc_start: 0.9137 (m-30) cc_final: 0.8780 (t0) REVERT: A 371 MET cc_start: 0.9527 (tmm) cc_final: 0.9135 (tmm) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.5555 time to fit residues: 54.3417 Evaluate side-chains 71 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 138 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.8673 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7787 Z= 0.286 Angle : 0.498 6.412 10542 Z= 0.264 Chirality : 0.035 0.120 1149 Planarity : 0.004 0.045 1348 Dihedral : 4.526 50.506 1018 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.20 % Allowed : 10.41 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.80 (0.28), residues: 915 helix: 2.62 (0.21), residues: 572 sheet: -0.76 (1.34), residues: 16 loop : 0.69 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 638 HIS 0.004 0.001 HIS A 498 PHE 0.019 0.001 PHE A 292 TYR 0.010 0.001 TYR A 228 ARG 0.008 0.001 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8298 (tptp) cc_final: 0.8073 (tptp) REVERT: A 60 ASP cc_start: 0.9104 (m-30) cc_final: 0.8183 (t0) REVERT: A 242 ASP cc_start: 0.9193 (m-30) cc_final: 0.8753 (t0) REVERT: A 371 MET cc_start: 0.9552 (tmm) cc_final: 0.9182 (tmm) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.5164 time to fit residues: 48.7161 Evaluate side-chains 66 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 73 optimal weight: 0.0070 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7787 Z= 0.177 Angle : 0.459 5.342 10542 Z= 0.238 Chirality : 0.034 0.121 1149 Planarity : 0.003 0.032 1348 Dihedral : 4.508 49.995 1018 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.96 % Allowed : 10.77 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.16 (0.29), residues: 915 helix: 2.89 (0.21), residues: 569 sheet: -0.41 (1.35), residues: 16 loop : 0.89 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 638 HIS 0.004 0.001 HIS A 498 PHE 0.013 0.001 PHE A 104 TYR 0.006 0.001 TYR A 169 ARG 0.003 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8297 (tptp) cc_final: 0.8073 (tptp) REVERT: A 60 ASP cc_start: 0.9114 (m-30) cc_final: 0.8187 (t0) REVERT: A 242 ASP cc_start: 0.9180 (m-30) cc_final: 0.8753 (t0) REVERT: A 371 MET cc_start: 0.9532 (tmm) cc_final: 0.9204 (tmm) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.5100 time to fit residues: 45.5144 Evaluate side-chains 64 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7787 Z= 0.150 Angle : 0.443 5.107 10542 Z= 0.229 Chirality : 0.034 0.123 1149 Planarity : 0.003 0.031 1348 Dihedral : 4.505 51.753 1018 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.72 % Allowed : 11.00 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.43 (0.29), residues: 915 helix: 3.04 (0.22), residues: 571 sheet: -0.06 (1.34), residues: 16 loop : 1.09 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 416 HIS 0.003 0.001 HIS A 498 PHE 0.014 0.001 PHE A 104 TYR 0.006 0.001 TYR B 138 ARG 0.003 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8292 (tptp) cc_final: 0.8065 (tptp) REVERT: A 60 ASP cc_start: 0.9105 (m-30) cc_final: 0.8172 (t0) REVERT: A 242 ASP cc_start: 0.9168 (m-30) cc_final: 0.8751 (t0) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.5363 time to fit residues: 45.2811 Evaluate side-chains 64 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7787 Z= 0.152 Angle : 0.444 5.654 10542 Z= 0.228 Chirality : 0.034 0.121 1149 Planarity : 0.003 0.034 1348 Dihedral : 4.516 54.022 1018 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.84 % Allowed : 10.89 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.45 (0.29), residues: 915 helix: 3.04 (0.21), residues: 577 sheet: 0.07 (1.32), residues: 16 loop : 1.08 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 416 HIS 0.003 0.001 HIS A 498 PHE 0.014 0.001 PHE A 104 TYR 0.006 0.001 TYR A 169 ARG 0.002 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8320 (tptp) cc_final: 0.8080 (tptp) REVERT: A 60 ASP cc_start: 0.9112 (m-30) cc_final: 0.8181 (t0) REVERT: A 242 ASP cc_start: 0.9176 (m-30) cc_final: 0.8756 (t0) REVERT: A 752 LEU cc_start: 0.9534 (mt) cc_final: 0.9237 (mt) outliers start: 7 outliers final: 7 residues processed: 65 average time/residue: 0.5442 time to fit residues: 47.1857 Evaluate side-chains 66 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7787 Z= 0.179 Angle : 0.453 5.938 10542 Z= 0.235 Chirality : 0.034 0.119 1149 Planarity : 0.003 0.032 1348 Dihedral : 4.543 55.758 1018 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.84 % Allowed : 11.12 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.45 (0.29), residues: 915 helix: 3.03 (0.21), residues: 577 sheet: 0.10 (1.31), residues: 16 loop : 1.09 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 638 HIS 0.003 0.001 HIS A 498 PHE 0.016 0.001 PHE A 104 TYR 0.006 0.001 TYR A 228 ARG 0.003 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8299 (tptp) cc_final: 0.8058 (tptp) REVERT: A 60 ASP cc_start: 0.9117 (m-30) cc_final: 0.8154 (t0) REVERT: A 242 ASP cc_start: 0.9182 (m-30) cc_final: 0.8755 (t0) REVERT: A 752 LEU cc_start: 0.9551 (mt) cc_final: 0.9242 (mt) outliers start: 7 outliers final: 7 residues processed: 64 average time/residue: 0.5200 time to fit residues: 44.0462 Evaluate side-chains 66 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7787 Z= 0.165 Angle : 0.450 4.801 10542 Z= 0.232 Chirality : 0.034 0.120 1149 Planarity : 0.003 0.033 1348 Dihedral : 4.571 58.141 1018 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.84 % Allowed : 11.12 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.50 (0.29), residues: 915 helix: 3.06 (0.21), residues: 578 sheet: 0.19 (1.32), residues: 16 loop : 1.13 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 638 HIS 0.003 0.001 HIS A 498 PHE 0.018 0.001 PHE A 104 TYR 0.006 0.001 TYR A 228 ARG 0.002 0.000 ARG A 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8312 (tptp) cc_final: 0.8070 (tptp) REVERT: A 60 ASP cc_start: 0.9115 (m-30) cc_final: 0.8189 (t0) REVERT: A 752 LEU cc_start: 0.9548 (mt) cc_final: 0.9233 (mt) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.5367 time to fit residues: 46.4560 Evaluate side-chains 64 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.044024 restraints weight = 87586.671| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.96 r_work: 0.2572 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7787 Z= 0.175 Angle : 0.454 6.333 10542 Z= 0.235 Chirality : 0.034 0.119 1149 Planarity : 0.003 0.032 1348 Dihedral : 4.599 59.900 1018 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.72 % Allowed : 11.00 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3.46 (0.29), residues: 915 helix: 3.02 (0.21), residues: 579 sheet: 0.20 (1.31), residues: 16 loop : 1.12 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 638 HIS 0.003 0.001 HIS A 498 PHE 0.010 0.001 PHE A 104 TYR 0.006 0.001 TYR A 228 ARG 0.003 0.000 ARG A 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3517.78 seconds wall clock time: 63 minutes 12.22 seconds (3792.22 seconds total)