Starting phenix.real_space_refine (version: dev) on Sat Feb 18 15:47:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/02_2023/7ozv_13138_updated.pdb" } resolution = 3.2 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= -0.000 sd= 0.002 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 Process input model Symmetric amino acids flipped Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8409 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6565 Classifications: {'peptide': 814} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 786} Chain breaks: 3 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1692 SG CYS A 301 47.732 66.352 36.395 1.00 55.92 S ATOM 1733 SG CYS A 306 47.334 65.879 32.523 1.00 52.97 S ATOM 1765 SG CYS A 310 50.364 65.588 34.819 1.00 49.18 S ATOM 3132 SG CYS A 487 30.327 62.531 45.778 1.00 62.63 S ATOM 4385 SG CYS A 645 28.837 62.401 41.815 1.00 65.93 S ATOM 4391 SG CYS A 646 31.679 64.363 43.369 1.00 60.57 S Time building chain proxies: 5.32, per 1000 atoms: 0.63 Number of scatterers: 8409 At special positions: 0 Unit cell: (91.74, 93.408, 99.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 57 16.00 P 22 15.00 O 1639 8.00 N 1405 7.00 C 5284 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: 3.14 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 46.2% alpha, 10.1% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.015A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.032A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.784A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.718A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 5.758A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.637A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 854 through 863 Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 895 removed outlier: 3.870A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.132A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 45 through 60 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.497A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.260A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.065A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1332 1.31 - 1.43: 2522 1.43 - 1.56: 4657 1.56 - 1.69: 46 1.69 - 1.81: 86 Bond restraints: 8643 Sorted by residual: bond pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 1.412 1.625 -0.213 1.50e-02 4.44e+03 2.01e+02 bond pdb=" C2' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 1.529 1.345 0.184 1.50e-02 4.44e+03 1.51e+02 bond pdb=" C4' 16B T 9 " pdb=" O4' 16B T 9 " ideal model delta sigma weight residual 1.451 1.299 0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" C2 16B T 9 " pdb=" N3 16B T 9 " ideal model delta sigma weight residual 1.520 1.327 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" P 16B T 9 " pdb=" OP2 16B T 9 " ideal model delta sigma weight residual 1.490 1.653 -0.163 2.00e-02 2.50e+03 6.60e+01 ... (remaining 8638 not shown) Histogram of bond angle deviations from ideal: 92.06 - 100.45: 13 100.45 - 108.84: 636 108.84 - 117.23: 5508 117.23 - 125.62: 5493 125.62 - 134.01: 183 Bond angle restraints: 11833 Sorted by residual: angle pdb=" O3' 16B T 9 " pdb=" P A T 10 " pdb=" O5' A T 10 " ideal model delta sigma weight residual 104.00 92.06 11.94 1.50e+00 4.44e-01 6.33e+01 angle pdb=" C2' 16B T 9 " pdb=" C1' 16B T 9 " pdb=" N1 16B T 9 " ideal model delta sigma weight residual 112.00 121.73 -9.73 1.50e+00 4.44e-01 4.21e+01 angle pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " pdb=" N1 16B T 9 " ideal model delta sigma weight residual 108.50 100.62 7.88 1.50e+00 4.44e-01 2.76e+01 angle pdb=" O3' 16B T 9 " pdb=" P A T 10 " pdb=" OP1 A T 10 " ideal model delta sigma weight residual 108.00 122.71 -14.71 3.00e+00 1.11e-01 2.40e+01 angle pdb=" C4' 16B T 9 " pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 109.90 105.90 4.00 1.00e+00 1.00e+00 1.60e+01 ... (remaining 11828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 4586 16.85 - 33.70: 387 33.70 - 50.55: 75 50.55 - 67.39: 13 67.39 - 84.24: 8 Dihedral angle restraints: 5069 sinusoidal: 2129 harmonic: 2940 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASP A 608 " pdb=" CB ASP A 608 " pdb=" CG ASP A 608 " pdb=" OD1 ASP A 608 " ideal model delta sinusoidal sigma weight residual -30.00 -89.96 59.96 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1249 0.078 - 0.156: 93 0.156 - 0.235: 0 0.235 - 0.313: 0 0.313 - 0.391: 1 Chirality restraints: 1343 Sorted by residual: chirality pdb=" C2' 16B T 9 " pdb=" C3' 16B T 9 " pdb=" O2' 16B T 9 " pdb=" C1' 16B T 9 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA VAL B 160 " pdb=" N VAL B 160 " pdb=" C VAL B 160 " pdb=" CB VAL B 160 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE A 757 " pdb=" N ILE A 757 " pdb=" C ILE A 757 " pdb=" CB ILE A 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1340 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 16B T 9 " -0.096 2.00e-02 2.50e+03 1.37e-01 4.70e+02 pdb=" N1 16B T 9 " -0.010 2.00e-02 2.50e+03 pdb=" C2 16B T 9 " -0.017 2.00e-02 2.50e+03 pdb=" O2 16B T 9 " -0.078 2.00e-02 2.50e+03 pdb=" N3 16B T 9 " 0.047 2.00e-02 2.50e+03 pdb=" C4 16B T 9 " 0.117 2.00e-02 2.50e+03 pdb=" N4 16B T 9 " 0.184 2.00e-02 2.50e+03 pdb=" C5 16B T 9 " 0.120 2.00e-02 2.50e+03 pdb=" C6 16B T 9 " 0.057 2.00e-02 2.50e+03 pdb=" OAC 16B T 9 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C LEU A 758 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 120 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO B 121 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.024 5.00e-02 4.00e+02 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 800 2.74 - 3.28: 8422 3.28 - 3.82: 14203 3.82 - 4.36: 17753 4.36 - 4.90: 29639 Nonbonded interactions: 70817 Sorted by model distance: nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR A 710 " pdb=" O GLY A 774 " model vdw 2.210 2.440 nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.219 2.440 nonbonded pdb=" OG SER A 318 " pdb=" O ARG A 349 " model vdw 2.236 2.440 ... (remaining 70812 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 22 5.49 5 S 57 5.16 5 C 5284 2.51 5 N 1405 2.21 5 O 1639 1.98 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.710 Check model and map are aligned: 0.130 Process input model: 28.300 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.213 8643 Z= 0.455 Angle : 0.583 14.712 11833 Z= 0.318 Chirality : 0.042 0.391 1343 Planarity : 0.005 0.137 1425 Dihedral : 13.231 84.243 3171 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.22 (0.26), residues: 979 helix: 0.20 (0.23), residues: 471 sheet: -0.05 (0.53), residues: 102 loop : -0.40 (0.30), residues: 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.920 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1942 time to fit residues: 33.0303 Evaluate side-chains 87 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8643 Z= 0.262 Angle : 0.523 6.736 11833 Z= 0.273 Chirality : 0.041 0.138 1343 Planarity : 0.004 0.038 1425 Dihedral : 6.645 53.559 1333 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.26), residues: 979 helix: 0.23 (0.23), residues: 472 sheet: -0.25 (0.54), residues: 100 loop : -0.35 (0.30), residues: 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.954 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.1849 time to fit residues: 25.1252 Evaluate side-chains 90 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0806 time to fit residues: 2.2228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.053 8643 Z= 0.497 Angle : 0.659 7.587 11833 Z= 0.347 Chirality : 0.047 0.156 1343 Planarity : 0.005 0.048 1425 Dihedral : 7.158 55.348 1333 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.89 (0.25), residues: 979 helix: -0.28 (0.23), residues: 469 sheet: -0.57 (0.52), residues: 103 loop : -0.79 (0.29), residues: 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.966 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.2044 time to fit residues: 28.0426 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0880 time to fit residues: 2.7157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8643 Z= 0.209 Angle : 0.489 6.473 11833 Z= 0.257 Chirality : 0.039 0.137 1343 Planarity : 0.003 0.039 1425 Dihedral : 7.025 59.001 1333 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.27 (0.26), residues: 979 helix: 0.22 (0.23), residues: 462 sheet: -0.23 (0.55), residues: 94 loop : -0.46 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.932 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 99 average time/residue: 0.1937 time to fit residues: 27.9250 Evaluate side-chains 90 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0828 time to fit residues: 1.7513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 8643 Z= 0.478 Angle : 0.634 7.316 11833 Z= 0.334 Chirality : 0.046 0.141 1343 Planarity : 0.004 0.048 1425 Dihedral : 7.314 57.722 1333 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.90 (0.25), residues: 979 helix: -0.28 (0.23), residues: 468 sheet: -0.61 (0.56), residues: 90 loop : -0.79 (0.28), residues: 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.954 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 0.2034 time to fit residues: 30.0915 Evaluate side-chains 95 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1463 time to fit residues: 3.5110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 0.0370 chunk 80 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8643 Z= 0.137 Angle : 0.447 6.042 11833 Z= 0.238 Chirality : 0.038 0.137 1343 Planarity : 0.003 0.036 1425 Dihedral : 7.035 63.221 1333 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.12 (0.26), residues: 979 helix: 0.33 (0.23), residues: 469 sheet: -0.17 (0.55), residues: 94 loop : -0.37 (0.30), residues: 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.929 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 98 average time/residue: 0.2028 time to fit residues: 28.5907 Evaluate side-chains 90 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0997 time to fit residues: 1.5320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8643 Z= 0.268 Angle : 0.507 6.398 11833 Z= 0.267 Chirality : 0.040 0.145 1343 Planarity : 0.004 0.038 1425 Dihedral : 6.965 62.812 1333 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.19 (0.26), residues: 979 helix: 0.25 (0.23), residues: 471 sheet: -0.14 (0.56), residues: 94 loop : -0.41 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.008 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 92 average time/residue: 0.1980 time to fit residues: 26.7274 Evaluate side-chains 88 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0735 time to fit residues: 1.4350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8643 Z= 0.164 Angle : 0.448 5.889 11833 Z= 0.236 Chirality : 0.038 0.143 1343 Planarity : 0.003 0.037 1425 Dihedral : 6.848 66.207 1333 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.01 (0.26), residues: 979 helix: 0.42 (0.23), residues: 471 sheet: -0.10 (0.56), residues: 94 loop : -0.30 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.016 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2044 time to fit residues: 27.6999 Evaluate side-chains 89 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 8643 Z= 0.354 Angle : 0.556 6.569 11833 Z= 0.293 Chirality : 0.042 0.141 1343 Planarity : 0.004 0.040 1425 Dihedral : 6.989 65.257 1333 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.35 (0.26), residues: 979 helix: 0.11 (0.23), residues: 470 sheet: -0.24 (0.56), residues: 94 loop : -0.46 (0.29), residues: 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.946 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 0.1933 time to fit residues: 26.1903 Evaluate side-chains 87 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0836 time to fit residues: 1.4616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8643 Z= 0.159 Angle : 0.456 5.829 11833 Z= 0.240 Chirality : 0.038 0.142 1343 Planarity : 0.003 0.037 1425 Dihedral : 6.823 69.362 1333 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.02 (0.26), residues: 979 helix: 0.41 (0.23), residues: 471 sheet: -0.12 (0.56), residues: 94 loop : -0.32 (0.30), residues: 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.826 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1847 time to fit residues: 24.5479 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115487 restraints weight = 9549.174| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.38 r_work: 0.3218 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8643 Z= 0.153 Angle : 0.442 5.701 11833 Z= 0.232 Chirality : 0.038 0.139 1343 Planarity : 0.003 0.035 1425 Dihedral : 6.623 71.472 1333 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.16 (0.26), residues: 979 helix: 0.55 (0.24), residues: 472 sheet: -0.01 (0.57), residues: 94 loop : -0.23 (0.30), residues: 413 =============================================================================== Job complete usr+sys time: 1728.56 seconds wall clock time: 32 minutes 30.35 seconds (1950.35 seconds total)