Starting phenix.real_space_refine (version: dev) on Fri May 13 22:47:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/05_2022/7lyt_23601_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.298 sd= 1.017 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 14354 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 11358 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 41, 'TRANS': 670} Chain: "B" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1259 Classifications: {'RNA': 39} Modifications used: {'rna3p_pyr': 15, 'rna2p_pur': 4, 'rna3p_pur': 18, 'rna2p_pyr': 2} Link IDs: {'rna3p': 32, 'rna2p': 6} Chain: "C" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1045 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 689 Unusual residues: {' SC': 3} Classifications: {'undetermined': 3, 'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {None: 3, 'rna3p': 19} Not linked: pdbres=" DA D 10 " pdbres=" SC D 11 " Not linked: pdbres=" SC D 11 " pdbres=" SC D 12 " Not linked: pdbres=" SC D 12 " pdbres=" SC D 13 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10645 SG CYS A 667 19.951 34.452 36.126 1.00 74.36 S ATOM 10691 SG CYS A 670 19.371 30.891 34.874 1.00 74.35 S ATOM 10893 SG CYS A 685 20.918 33.488 32.615 1.00 72.22 S ATOM 10933 SG CYS A 688 17.233 33.644 33.534 1.00 73.11 S Time building chain proxies: 7.48, per 1000 atoms: 0.52 Number of scatterers: 14354 At special positions: 0 Unit cell: (88.085, 98.12, 124.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 24 16.00 P 94 15.00 Mg 2 11.99 O 1644 8.00 N 1392 7.00 C 4475 6.00 H 6722 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 685 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 670 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 688 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 667 " Number of angles added : 6 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 4 sheets defined 39.2% alpha, 7.7% beta 21 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 25 through 38 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 44 through 47 No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 126 through 168 removed outlier: 3.882A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.513A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 372 through 382 removed outlier: 3.513A pdb=" N THR A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.901A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 550 through 565 Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.751A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.686A pdb=" N ARG A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 707 Processing sheet with id= A, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.583A pdb=" N HIS A 65 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 310 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS A 69 " --> pdb=" O TRP A 308 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP A 308 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.705A pdb=" N ALA A 261 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 388 through 395 removed outlier: 6.163A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 603 through 606 211 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 13.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 6711 1.09 - 1.35: 2334 1.35 - 1.61: 5600 1.61 - 1.86: 55 1.86 - 2.12: 3 Bond restraints: 14703 Sorted by residual: bond pdb=" C4' SC D 13 " pdb=" O4' SC D 13 " ideal model delta sigma weight residual 1.295 1.623 -0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" C4' SC D 11 " pdb=" O4' SC D 11 " ideal model delta sigma weight residual 1.295 1.622 -0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C4' SC D 12 " pdb=" O4' SC D 12 " ideal model delta sigma weight residual 1.295 1.619 -0.324 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C3' SC D 11 " pdb=" C4' SC D 11 " ideal model delta sigma weight residual 1.619 1.303 0.316 2.00e-02 2.50e+03 2.49e+02 bond pdb=" C3' SC D 13 " pdb=" C4' SC D 13 " ideal model delta sigma weight residual 1.619 1.311 0.308 2.00e-02 2.50e+03 2.37e+02 ... (remaining 14698 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 805 106.92 - 113.70: 16705 113.70 - 120.48: 5273 120.48 - 127.25: 3564 127.25 - 134.03: 227 Bond angle restraints: 26574 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 104.87 -3.27 1.50e+00 4.44e-01 4.75e+00 angle pdb=" C3' DC C -6 " pdb=" C2' DC C -6 " pdb=" C1' DC C -6 " ideal model delta sigma weight residual 101.60 104.48 -2.88 1.50e+00 4.44e-01 3.69e+00 angle pdb=" N ALA A 74 " pdb=" CA ALA A 74 " pdb=" C ALA A 74 " ideal model delta sigma weight residual 113.29 109.54 3.75 2.00e+00 2.50e-01 3.52e+00 angle pdb=" C LYS A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 120.53 125.13 -4.60 2.52e+00 1.57e-01 3.33e+00 angle pdb=" N THR A 409 " pdb=" CA THR A 409 " pdb=" C THR A 409 " ideal model delta sigma weight residual 109.81 107.07 2.74 1.53e+00 4.27e-01 3.20e+00 ... (remaining 26569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 5422 34.33 - 68.65: 288 68.65 - 102.98: 27 102.98 - 137.30: 0 137.30 - 171.63: 2 Dihedral angle restraints: 5739 sinusoidal: 3352 harmonic: 2387 Sorted by residual: dihedral pdb=" O4' G B -20 " pdb=" C1' G B -20 " pdb=" N9 G B -20 " pdb=" C4 G B -20 " ideal model delta sinusoidal sigma weight residual 68.00 144.05 -76.05 1 1.70e+01 3.46e-03 2.52e+01 dihedral pdb=" CA GLN A 410 " pdb=" C GLN A 410 " pdb=" N GLU A 411 " pdb=" CA GLU A 411 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DC D -7 " ideal model delta sinusoidal sigma weight residual 220.00 48.37 171.63 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 757 0.026 - 0.051: 333 0.051 - 0.077: 101 0.077 - 0.102: 46 0.102 - 0.128: 23 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 351 " pdb=" N ILE A 351 " pdb=" C ILE A 351 " pdb=" CB ILE A 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL A 601 " pdb=" N VAL A 601 " pdb=" C VAL A 601 " pdb=" CB VAL A 601 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1257 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' SC D 11 " 0.174 2.00e-02 2.50e+03 5.96e-01 7.11e+03 pdb=" C2' SC D 11 " -1.038 2.00e-02 2.50e+03 pdb=" C3' SC D 11 " -0.424 2.00e-02 2.50e+03 pdb=" C4' SC D 11 " 0.418 2.00e-02 2.50e+03 pdb=" C5' SC D 11 " -0.352 2.00e-02 2.50e+03 pdb=" N1 SC D 11 " -0.159 2.00e-02 2.50e+03 pdb=" O3' SC D 11 " 0.314 2.00e-02 2.50e+03 pdb=" O4' SC D 11 " 1.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SC D 13 " 0.291 2.00e-02 2.50e+03 5.42e-01 5.88e+03 pdb=" C2' SC D 13 " -0.901 2.00e-02 2.50e+03 pdb=" C3' SC D 13 " -0.390 2.00e-02 2.50e+03 pdb=" C4' SC D 13 " 0.366 2.00e-02 2.50e+03 pdb=" C5' SC D 13 " -0.448 2.00e-02 2.50e+03 pdb=" N1 SC D 13 " -0.206 2.00e-02 2.50e+03 pdb=" O3' SC D 13 " 0.426 2.00e-02 2.50e+03 pdb=" O4' SC D 13 " 0.863 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SC D 12 " 0.404 2.00e-02 2.50e+03 3.54e-01 2.51e+03 pdb=" C2' SC D 12 " -0.337 2.00e-02 2.50e+03 pdb=" C3' SC D 12 " -0.358 2.00e-02 2.50e+03 pdb=" C4' SC D 12 " 0.330 2.00e-02 2.50e+03 pdb=" C5' SC D 12 " -0.401 2.00e-02 2.50e+03 pdb=" N1 SC D 12 " -0.311 2.00e-02 2.50e+03 pdb=" O3' SC D 12 " 0.284 2.00e-02 2.50e+03 pdb=" O4' SC D 12 " 0.388 2.00e-02 2.50e+03 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 681 2.17 - 2.78: 26188 2.78 - 3.39: 38073 3.39 - 3.99: 50273 3.99 - 4.60: 76154 Nonbonded interactions: 191369 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 146 " pdb=" O2 DC C -5 " model vdw 1.565 1.850 nonbonded pdb="HH22 ARG A 542 " pdb=" O6 DG C -18 " model vdw 1.569 1.850 nonbonded pdb=" OE1 GLU A 7 " pdb=" H GLU A 7 " model vdw 1.604 1.850 nonbonded pdb=" HG1 THR A 340 " pdb=" OP2 DT C 0 " model vdw 1.607 1.850 nonbonded pdb=" O LEU A 14 " pdb=" H PHE A 18 " model vdw 1.625 1.850 ... (remaining 191364 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 Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 94 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 4475 2.51 5 N 1392 2.21 5 O 1644 1.98 5 H 6722 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.390 Extract box with map and model: 3.080 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.130 Process input model: 57.750 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.014 0.328 7981 Z= 0.709 Angle : 0.551 7.501 11217 Z= 0.312 Chirality : 0.036 0.128 1260 Planarity : 0.027 0.596 1116 Dihedral : 18.872 171.627 3222 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 710 helix: -0.04 (0.30), residues: 281 sheet: -1.48 (0.64), residues: 62 loop : -1.83 (0.28), residues: 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 1.7993 time to fit residues: 226.8081 Evaluate side-chains 84 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 7981 Z= 0.237 Angle : 0.849 18.937 11217 Z= 0.383 Chirality : 0.039 0.127 1260 Planarity : 0.005 0.075 1116 Dihedral : 19.210 172.037 1806 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.30), residues: 710 helix: 0.64 (0.30), residues: 286 sheet: -1.19 (0.66), residues: 62 loop : -1.49 (0.30), residues: 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 1.6088 time to fit residues: 156.2084 Evaluate side-chains 85 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.2064 time to fit residues: 2.2320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 7981 Z= 0.313 Angle : 0.849 17.525 11217 Z= 0.388 Chirality : 0.041 0.136 1260 Planarity : 0.005 0.056 1116 Dihedral : 19.414 171.258 1806 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.30), residues: 710 helix: 0.56 (0.30), residues: 289 sheet: -1.27 (0.65), residues: 62 loop : -1.63 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 87 average time/residue: 1.5765 time to fit residues: 149.6347 Evaluate side-chains 85 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.5228 time to fit residues: 4.5257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 7981 Z= 0.206 Angle : 0.808 16.344 11217 Z= 0.362 Chirality : 0.038 0.132 1260 Planarity : 0.004 0.062 1116 Dihedral : 19.308 170.133 1806 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.31), residues: 710 helix: 0.92 (0.30), residues: 291 sheet: -1.27 (0.66), residues: 60 loop : -1.37 (0.31), residues: 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 91 average time/residue: 1.6207 time to fit residues: 160.7626 Evaluate side-chains 82 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.6034 time to fit residues: 4.0945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 7981 Z= 0.292 Angle : 0.834 16.497 11217 Z= 0.379 Chirality : 0.041 0.131 1260 Planarity : 0.005 0.058 1116 Dihedral : 19.397 169.100 1806 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.31), residues: 710 helix: 0.79 (0.30), residues: 292 sheet: -1.25 (0.66), residues: 60 loop : -1.52 (0.31), residues: 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 92 average time/residue: 1.6686 time to fit residues: 166.7837 Evaluate side-chains 85 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.6504 time to fit residues: 4.3069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 7981 Z= 0.260 Angle : 0.822 16.358 11217 Z= 0.371 Chirality : 0.040 0.130 1260 Planarity : 0.004 0.035 1116 Dihedral : 19.422 168.676 1806 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.31), residues: 710 helix: 0.84 (0.30), residues: 292 sheet: -1.22 (0.65), residues: 60 loop : -1.49 (0.31), residues: 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 1.6617 time to fit residues: 171.7646 Evaluate side-chains 91 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.4392 time to fit residues: 5.2039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.8080 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7981 Z= 0.220 Angle : 0.809 16.040 11217 Z= 0.362 Chirality : 0.039 0.128 1260 Planarity : 0.004 0.034 1116 Dihedral : 19.360 168.776 1806 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.31), residues: 710 helix: 0.98 (0.31), residues: 292 sheet: -1.19 (0.61), residues: 67 loop : -1.52 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 1.6168 time to fit residues: 162.0363 Evaluate side-chains 86 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.0879 time to fit residues: 3.6094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8050 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7981 Z= 0.166 Angle : 0.791 15.491 11217 Z= 0.352 Chirality : 0.037 0.126 1260 Planarity : 0.004 0.036 1116 Dihedral : 19.191 169.020 1806 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.32), residues: 710 helix: 1.33 (0.31), residues: 292 sheet: -1.23 (0.59), residues: 71 loop : -1.31 (0.33), residues: 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 1.6912 time to fit residues: 179.9098 Evaluate side-chains 86 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.3620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 7981 Z= 0.310 Angle : 0.834 16.160 11217 Z= 0.378 Chirality : 0.041 0.130 1260 Planarity : 0.004 0.035 1116 Dihedral : 19.345 167.675 1806 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.32), residues: 710 helix: 0.96 (0.31), residues: 293 sheet: -1.31 (0.58), residues: 72 loop : -1.49 (0.33), residues: 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 92 average time/residue: 1.5311 time to fit residues: 154.4936 Evaluate side-chains 93 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.6951 time to fit residues: 4.5667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8053 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7981 Z= 0.161 Angle : 0.794 15.555 11217 Z= 0.353 Chirality : 0.037 0.122 1260 Planarity : 0.004 0.036 1116 Dihedral : 19.217 168.697 1806 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.32), residues: 710 helix: 1.35 (0.31), residues: 292 sheet: -1.35 (0.57), residues: 76 loop : -1.24 (0.34), residues: 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 97 average time/residue: 1.4854 time to fit residues: 158.6615 Evaluate side-chains 92 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.2366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.092119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083648 restraints weight = 46776.038| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.59 r_work: 0.3245 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.3224 rms_B_bonded: 1.53 restraints_weight: 0.1250 r_work: 0.3213 rms_B_bonded: 1.68 restraints_weight: 0.0625 r_work: 0.3200 rms_B_bonded: 1.88 restraints_weight: 0.0312 r_work: 0.3186 rms_B_bonded: 2.13 restraints_weight: 0.0156 r_work: 0.3170 rms_B_bonded: 2.44 restraints_weight: 0.0078 r_work: 0.3152 rms_B_bonded: 2.82 restraints_weight: 0.0039 r_work: 0.3132 rms_B_bonded: 3.27 restraints_weight: 0.0020 r_work: 0.3109 rms_B_bonded: 3.81 restraints_weight: 0.0010 r_work: 0.3083 rms_B_bonded: 4.45 restraints_weight: 0.0005 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7981 Z= 0.185 Angle : 0.795 15.533 11217 Z= 0.353 Chirality : 0.038 0.125 1260 Planarity : 0.004 0.037 1116 Dihedral : 19.159 168.357 1806 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.32), residues: 710 helix: 1.40 (0.31), residues: 292 sheet: -1.30 (0.57), residues: 76 loop : -1.22 (0.34), residues: 342 =============================================================================== Job complete usr+sys time: 4632.38 seconds wall clock time: 81 minutes 58.55 seconds (4918.55 seconds total)