Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 04:10:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/08_2023/8hhl_34803.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/08_2023/8hhl_34803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/08_2023/8hhl_34803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/08_2023/8hhl_34803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/08_2023/8hhl_34803.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhl_34803/08_2023/8hhl_34803.pdb" } resolution = 2.87 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 ------------------------------------------------------------------------------- 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= -0.012 sd= 0.253 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 111 5.49 5 Mg 3 5.21 5 S 19 5.16 5 C 3939 2.51 5 N 1321 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 6971 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1066 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 28, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 43} Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 624 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4630 Classifications: {'peptide': 592} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 567} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6663 SG CYS A 552 87.861 24.922 31.530 1.00120.60 S ATOM 6796 SG CYS A 569 84.715 23.574 29.746 1.00120.99 S ATOM 6814 SG CYS A 572 86.921 21.084 31.118 1.00121.86 S Time building chain proxies: 4.46, per 1000 atoms: 0.64 Number of scatterers: 6971 At special positions: 0 Unit cell: (101.094, 89.474, 103.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 111 15.00 Mg 3 11.99 O 1577 8.00 N 1321 7.00 C 3939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 664.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 569 " Number of angles added : 3 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 58.1% alpha, 14.4% beta 40 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 18 through 52 Processing helix chain 'A' and resid 53 through 85 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.558A pdb=" N THR A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 176 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.605A pdb=" N LEU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 362 through 397 removed outlier: 4.195A pdb=" N GLU A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.230A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 479 removed outlier: 3.520A pdb=" N TRP A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 4.495A pdb=" N MET A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.570A pdb=" N LEU A 563 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 579 through 591 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.076A pdb=" N ILE A 278 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG A 301 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 280 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 253 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 262 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A 251 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 264 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG A 249 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 266 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 247 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360 removed outlier: 4.813A pdb=" N THR A 327 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 321 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 329 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 567 through 568 300 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1580 1.33 - 1.45: 2077 1.45 - 1.57: 3432 1.57 - 1.69: 219 1.69 - 1.81: 31 Bond restraints: 7339 Sorted by residual: bond pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DT D -10 " pdb=" O3' DT D -10 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" C2' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 1.525 1.504 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CA ASP A 560 " pdb=" CB ASP A 560 " ideal model delta sigma weight residual 1.532 1.547 -0.015 1.51e-02 4.39e+03 9.66e-01 bond pdb=" O4' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.01e-01 ... (remaining 7334 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.77: 656 105.77 - 112.85: 4148 112.85 - 119.93: 2457 119.93 - 127.02: 2867 127.02 - 134.10: 342 Bond angle restraints: 10470 Sorted by residual: angle pdb=" C2' DG D 0 " pdb=" C1' DG D 0 " pdb=" N9 DG D 0 " ideal model delta sigma weight residual 113.50 117.07 -3.57 1.50e+00 4.44e-01 5.66e+00 angle pdb=" C ASP A 559 " pdb=" N ASP A 560 " pdb=" CA ASP A 560 " ideal model delta sigma weight residual 122.61 126.22 -3.61 1.56e+00 4.11e-01 5.36e+00 angle pdb=" C4' DG D 0 " pdb=" O4' DG D 0 " pdb=" C1' DG D 0 " ideal model delta sigma weight residual 109.70 106.45 3.25 1.50e+00 4.44e-01 4.70e+00 angle pdb=" CA ASP A 560 " pdb=" CB ASP A 560 " pdb=" CG ASP A 560 " ideal model delta sigma weight residual 112.60 114.65 -2.05 1.00e+00 1.00e+00 4.21e+00 angle pdb=" OP2 DT D -8 " pdb=" P DT D -8 " pdb=" O5' DT D -8 " ideal model delta sigma weight residual 108.00 102.09 5.91 3.00e+00 1.11e-01 3.88e+00 ... (remaining 10465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 3535 23.75 - 47.50: 377 47.50 - 71.25: 149 71.25 - 95.00: 7 95.00 - 118.75: 1 Dihedral angle restraints: 4069 sinusoidal: 2346 harmonic: 1723 Sorted by residual: dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -172.34 66.34 1 1.70e+01 3.46e-03 1.99e+01 dihedral pdb=" C4' DG D -9 " pdb=" C3' DG D -9 " pdb=" O3' DG D -9 " pdb=" P DT D -8 " ideal model delta sinusoidal sigma weight residual 220.00 101.25 118.75 1 3.50e+01 8.16e-04 1.16e+01 dihedral pdb=" CA ASP A 477 " pdb=" CB ASP A 477 " pdb=" CG ASP A 477 " pdb=" OD1 ASP A 477 " ideal model delta sinusoidal sigma weight residual -30.00 -86.97 56.97 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 4066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 889 0.033 - 0.066: 241 0.066 - 0.099: 58 0.099 - 0.133: 17 0.133 - 0.166: 5 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C1' DG D 0 " pdb=" O4' DG D 0 " pdb=" C2' DG D 0 " pdb=" N9 DG D 0 " both_signs ideal model delta sigma weight residual False 2.42 2.25 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ASP A 560 " pdb=" N ASP A 560 " pdb=" C ASP A 560 " pdb=" CB ASP A 560 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1207 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG D 0 " 0.027 2.00e-02 2.50e+03 1.15e-02 3.97e+00 pdb=" N9 DG D 0 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DG D 0 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG D 0 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 0 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 0 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG D 0 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG D 0 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG D 0 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG D 0 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG D 0 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 2 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.34e+00 pdb=" N9 G B 2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 2 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 2 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 2 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C GLN A 452 " -0.031 2.00e-02 2.50e+03 pdb=" O GLN A 452 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 453 " 0.010 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 215 2.68 - 3.24: 6117 3.24 - 3.79: 12497 3.79 - 4.35: 16282 4.35 - 4.90: 24625 Nonbonded interactions: 59736 Sorted by model distance: nonbonded pdb=" OD1 ASP A 579 " pdb="MG MG A 601 " model vdw 2.126 2.170 nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 2.134 2.170 nonbonded pdb=" OP1 DG D 15 " pdb="MG MG A 601 " model vdw 2.143 2.170 nonbonded pdb=" OG SER A 334 " pdb=" O ALA A 336 " model vdw 2.154 2.440 nonbonded pdb=" NE2 HIS A 317 " pdb="MG MG A 601 " model vdw 2.198 2.250 ... (remaining 59731 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.970 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.720 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.062 7339 Z= 0.217 Angle : 0.499 5.911 10470 Z= 0.284 Chirality : 0.035 0.166 1210 Planarity : 0.004 0.042 951 Dihedral : 19.768 118.750 2949 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.28 (0.35), residues: 590 helix: 2.63 (0.29), residues: 323 sheet: 1.62 (0.63), residues: 60 loop : -0.37 (0.41), residues: 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.646 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 82 average time/residue: 1.6636 time to fit residues: 141.9161 Evaluate side-chains 47 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 242 GLN A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 7339 Z= 0.249 Angle : 0.541 7.972 10470 Z= 0.300 Chirality : 0.037 0.169 1210 Planarity : 0.005 0.100 951 Dihedral : 20.454 117.699 1861 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.82 (0.34), residues: 590 helix: 3.18 (0.28), residues: 324 sheet: 1.63 (0.60), residues: 62 loop : -0.31 (0.41), residues: 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.625 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 1.6327 time to fit residues: 108.9675 Evaluate side-chains 50 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 2.0638 time to fit residues: 2.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 7339 Z= 0.296 Angle : 0.554 7.269 10470 Z= 0.306 Chirality : 0.038 0.174 1210 Planarity : 0.005 0.106 951 Dihedral : 20.534 117.207 1861 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.77 (0.34), residues: 590 helix: 3.13 (0.27), residues: 324 sheet: 1.48 (0.60), residues: 62 loop : -0.27 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.593 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 60 average time/residue: 1.5571 time to fit residues: 97.5960 Evaluate side-chains 49 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 2.2274 time to fit residues: 3.0853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 7339 Z= 0.285 Angle : 0.546 6.827 10470 Z= 0.303 Chirality : 0.038 0.167 1210 Planarity : 0.005 0.061 951 Dihedral : 20.562 116.471 1861 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.81 (0.34), residues: 590 helix: 3.16 (0.27), residues: 324 sheet: 1.47 (0.60), residues: 62 loop : -0.21 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 44 time to evaluate : 0.630 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 58 average time/residue: 1.6474 time to fit residues: 99.9143 Evaluate side-chains 51 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.6300 time to fit residues: 2.1024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 7339 Z= 0.263 Angle : 0.539 7.337 10470 Z= 0.299 Chirality : 0.037 0.161 1210 Planarity : 0.004 0.046 951 Dihedral : 20.588 115.219 1861 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.34), residues: 590 helix: 3.22 (0.27), residues: 324 sheet: 1.42 (0.59), residues: 62 loop : -0.20 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.558 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 56 average time/residue: 1.4612 time to fit residues: 85.8835 Evaluate side-chains 53 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.8101 time to fit residues: 3.3715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 0.0370 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 7339 Z= 0.256 Angle : 0.542 8.273 10470 Z= 0.299 Chirality : 0.037 0.156 1210 Planarity : 0.004 0.042 951 Dihedral : 20.573 114.194 1861 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.89 (0.34), residues: 590 helix: 3.26 (0.27), residues: 324 sheet: 1.43 (0.59), residues: 62 loop : -0.24 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.646 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 55 average time/residue: 1.3561 time to fit residues: 78.6887 Evaluate side-chains 53 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.4216 time to fit residues: 2.1965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 7339 Z= 0.316 Angle : 0.569 8.852 10470 Z= 0.312 Chirality : 0.038 0.159 1210 Planarity : 0.004 0.035 951 Dihedral : 20.687 114.973 1861 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.74 (0.34), residues: 590 helix: 3.13 (0.27), residues: 324 sheet: 1.42 (0.60), residues: 62 loop : -0.29 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.632 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 54 average time/residue: 1.4145 time to fit residues: 80.4482 Evaluate side-chains 51 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 1.7571 time to fit residues: 4.4348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 7339 Z= 0.164 Angle : 0.511 11.047 10470 Z= 0.281 Chirality : 0.034 0.140 1210 Planarity : 0.004 0.032 951 Dihedral : 20.511 110.670 1861 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.11 (0.34), residues: 590 helix: 3.51 (0.28), residues: 324 sheet: 1.46 (0.59), residues: 62 loop : -0.24 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.610 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 1.2983 time to fit residues: 78.2261 Evaluate side-chains 50 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0677 time to fit residues: 0.8544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 0.0470 chunk 45 optimal weight: 20.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 7339 Z= 0.318 Angle : 0.566 9.150 10470 Z= 0.309 Chirality : 0.038 0.192 1210 Planarity : 0.004 0.032 951 Dihedral : 20.590 112.627 1861 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.82 (0.34), residues: 590 helix: 3.20 (0.27), residues: 324 sheet: 1.41 (0.59), residues: 62 loop : -0.26 (0.42), residues: 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.637 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 51 average time/residue: 1.3401 time to fit residues: 72.1812 Evaluate side-chains 50 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.6420 time to fit residues: 4.1686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 7339 Z= 0.287 Angle : 0.576 11.147 10470 Z= 0.311 Chirality : 0.038 0.172 1210 Planarity : 0.004 0.035 951 Dihedral : 20.538 113.868 1861 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.34), residues: 590 helix: 3.16 (0.27), residues: 324 sheet: 1.44 (0.59), residues: 62 loop : -0.24 (0.42), residues: 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 49 average time/residue: 1.3234 time to fit residues: 68.5258 Evaluate side-chains 48 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.6984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104771 restraints weight = 9717.344| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.47 r_work: 0.3206 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 7339 Z= 0.241 Angle : 0.540 9.228 10470 Z= 0.298 Chirality : 0.036 0.164 1210 Planarity : 0.004 0.032 951 Dihedral : 20.512 112.915 1861 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.89 (0.34), residues: 590 helix: 3.25 (0.27), residues: 324 sheet: 1.46 (0.59), residues: 62 loop : -0.21 (0.42), residues: 204 =============================================================================== Job complete usr+sys time: 2139.27 seconds wall clock time: 38 minutes 52.35 seconds (2332.35 seconds total)