Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 22:05:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea8_31040/07_2023/7ea8_31040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea8_31040/07_2023/7ea8_31040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea8_31040/07_2023/7ea8_31040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea8_31040/07_2023/7ea8_31040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea8_31040/07_2023/7ea8_31040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea8_31040/07_2023/7ea8_31040_updated.pdb" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4902 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 244 5.49 5 S 33 5.16 5 C 7305 2.51 5 N 2401 2.21 5 O 2879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 1455": "NH1" <-> "NH2" Residue "L ARG 1598": "NH1" <-> "NH2" Residue "L ARG 1686": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 12865 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1993 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 818 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2485 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2517 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 643 SG CYS L1529 40.601 58.945 52.919 1.00 46.92 S ATOM 672 SG CYS L1533 40.198 62.627 55.544 1.00 53.00 S ATOM 717 SG CYS L1539 40.330 62.668 51.612 1.00 47.82 S ATOM 416 SG CYS L1499 43.510 60.073 56.178 1.00 47.21 S ATOM 431 SG CYS L1501 46.699 61.864 55.722 1.00 51.47 S ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 569 SG CYS L1520 45.259 58.912 52.403 1.00 43.65 S ATOM 1863 SG CYS L1678 39.772 46.170 17.879 1.00 67.56 S ATOM 1909 SG CYS L1685 43.414 44.340 16.211 1.00 57.15 S Time building chain proxies: 6.47, per 1000 atoms: 0.50 Number of scatterers: 12865 At special positions: 0 Unit cell: (132, 88, 141.9, 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 3 29.99 S 33 16.00 P 244 15.00 O 2879 8.00 N 2401 7.00 C 7305 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1801 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1539 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1533 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1529 " pdb=" ZN L1802 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1520 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1499 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1501 " pdb=" ZN L1803 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1678 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1685 " Number of angles added : 12 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 2 sheets defined 49.9% alpha, 1.8% beta 121 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'L' and resid 1521 through 1524 No H-bonds generated for 'chain 'L' and resid 1521 through 1524' Processing helix chain 'L' and resid 1586 through 1599 removed outlier: 4.643A pdb=" N LYS L1590 " --> pdb=" O HIS L1586 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L1591 " --> pdb=" O LYS L1587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS L1594 " --> pdb=" O LYS L1590 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG L1598 " --> pdb=" O LYS L1594 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN L1599 " --> pdb=" O GLU L1595 " (cutoff:3.500A) Processing helix chain 'L' and resid 1623 through 1625 No H-bonds generated for 'chain 'L' and resid 1623 through 1625' Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.849A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.738A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.706A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.815A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 83 removed outlier: 3.659A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 105 through 122 removed outlier: 3.591A pdb=" N THR D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.606A pdb=" N GLU E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.556A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.661A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 73 removed outlier: 3.914A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.912A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 83 removed outlier: 3.718A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.613A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 1606 through 1608 Processing sheet with id= B, first strand: chain 'L' and resid 1635 through 1642 330 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2951 1.34 - 1.46: 4033 1.46 - 1.58: 6070 1.58 - 1.70: 486 1.70 - 1.82: 49 Bond restraints: 13589 Sorted by residual: bond pdb=" C2 SAM L1804 " pdb=" N3 SAM L1804 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C8 SAM L1804 " pdb=" N7 SAM L1804 " ideal model delta sigma weight residual 1.298 1.353 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C2 SAM L1804 " pdb=" N1 SAM L1804 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C6 SAM L1804 " pdb=" N1 SAM L1804 " ideal model delta sigma weight residual 1.337 1.380 -0.043 2.00e-02 2.50e+03 4.64e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.82e+00 ... (remaining 13584 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.72: 1336 105.72 - 112.78: 7248 112.78 - 119.85: 4785 119.85 - 126.92: 5371 126.92 - 133.99: 635 Bond angle restraints: 19375 Sorted by residual: angle pdb=" N SER L1490 " pdb=" CA SER L1490 " pdb=" C SER L1490 " ideal model delta sigma weight residual 110.97 114.53 -3.56 1.09e+00 8.42e-01 1.07e+01 angle pdb=" N VAL D 48 " pdb=" CA VAL D 48 " pdb=" C VAL D 48 " ideal model delta sigma weight residual 113.39 108.67 4.72 1.47e+00 4.63e-01 1.03e+01 angle pdb=" C LYS L1489 " pdb=" N SER L1490 " pdb=" CA SER L1490 " ideal model delta sigma weight residual 120.65 124.65 -4.00 1.32e+00 5.74e-01 9.18e+00 angle pdb=" N1 SAM L1804 " pdb=" C2 SAM L1804 " pdb=" N3 SAM L1804 " ideal model delta sigma weight residual 128.51 120.03 8.48 3.00e+00 1.11e-01 8.00e+00 angle pdb=" O SAM L1804 " pdb=" C SAM L1804 " pdb=" OXT SAM L1804 " ideal model delta sigma weight residual 126.77 118.53 8.24 3.00e+00 1.11e-01 7.54e+00 ... (remaining 19370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 5989 27.88 - 55.77: 1233 55.77 - 83.65: 109 83.65 - 111.53: 0 111.53 - 139.41: 3 Dihedral angle restraints: 7334 sinusoidal: 4490 harmonic: 2844 Sorted by residual: dihedral pdb=" CA TYR L1666 " pdb=" C TYR L1666 " pdb=" N GLN L1667 " pdb=" CA GLN L1667 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLU L1478 " pdb=" C GLU L1478 " pdb=" N ASN L1479 " pdb=" CA ASN L1479 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 80.59 139.41 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 7331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1775 0.052 - 0.104: 326 0.104 - 0.156: 67 0.156 - 0.208: 4 0.208 - 0.260: 1 Chirality restraints: 2173 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE L1494 " pdb=" CA ILE L1494 " pdb=" CG1 ILE L1494 " pdb=" CG2 ILE L1494 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 2170 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 103 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO D 103 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3111 2.82 - 3.34: 10067 3.34 - 3.86: 22855 3.86 - 4.38: 26925 4.38 - 4.90: 39776 Nonbonded interactions: 102734 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.306 2.440 nonbonded pdb=" ND2 ASN L1634 " pdb=" O GLU L1661 " model vdw 2.379 2.520 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.381 2.520 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.382 2.440 nonbonded pdb=" O GLU L1578 " pdb=" ND2 ASN L1622 " model vdw 2.387 2.520 ... (remaining 102729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 76 or resid 78 through 133)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 4.220 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 41.430 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 13589 Z= 0.216 Angle : 0.709 8.483 19375 Z= 0.422 Chirality : 0.043 0.260 2173 Planarity : 0.006 0.051 1621 Dihedral : 24.028 139.413 5504 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.00 % 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: -3.23 (0.21), residues: 964 helix: -1.58 (0.17), residues: 540 sheet: -2.04 (0.90), residues: 31 loop : -2.88 (0.25), residues: 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.4458 time to fit residues: 131.0872 Evaluate side-chains 155 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1545 GLN L1548 GLN L1599 ASN ** L1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1667 GLN L1684 ASN A 39 HIS A 68 GLN B 93 GLN C 68 ASN D 109 HIS E 68 GLN E 113 HIS F 27 GLN H 47 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13589 Z= 0.163 Angle : 0.512 6.506 19375 Z= 0.305 Chirality : 0.034 0.140 2173 Planarity : 0.004 0.039 1621 Dihedral : 28.880 144.251 3545 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.33 % 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: -1.10 (0.25), residues: 964 helix: 0.63 (0.22), residues: 538 sheet: -1.97 (0.87), residues: 33 loop : -2.66 (0.26), residues: 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.044 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 162 average time/residue: 0.3857 time to fit residues: 80.2005 Evaluate side-chains 153 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2688 time to fit residues: 3.1806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1541 ASN B 27 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 13589 Z= 0.284 Angle : 0.580 6.186 19375 Z= 0.340 Chirality : 0.038 0.163 2173 Planarity : 0.005 0.056 1621 Dihedral : 29.042 146.105 3545 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.72 % 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: -0.81 (0.26), residues: 964 helix: 0.91 (0.22), residues: 544 sheet: -1.79 (0.91), residues: 28 loop : -2.65 (0.26), residues: 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.051 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 153 average time/residue: 0.4062 time to fit residues: 79.2234 Evaluate side-chains 146 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1137 time to fit residues: 1.9030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 13589 Z= 0.206 Angle : 0.527 6.013 19375 Z= 0.313 Chirality : 0.035 0.131 2173 Planarity : 0.004 0.044 1621 Dihedral : 28.985 146.892 3545 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.60 % 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 (0.27), residues: 964 helix: 1.47 (0.23), residues: 531 sheet: -1.68 (0.94), residues: 28 loop : -2.49 (0.26), residues: 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.298 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 148 average time/residue: 0.3715 time to fit residues: 71.5343 Evaluate side-chains 146 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1183 time to fit residues: 2.2107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 97 optimal weight: 8.9990 chunk 78 optimal weight: 0.0870 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1548 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 13589 Z= 0.340 Angle : 0.613 5.462 19375 Z= 0.357 Chirality : 0.039 0.178 2173 Planarity : 0.005 0.046 1621 Dihedral : 29.136 146.516 3545 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.48 % 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: -0.58 (0.26), residues: 964 helix: 1.16 (0.23), residues: 532 sheet: -1.92 (0.90), residues: 28 loop : -2.52 (0.26), residues: 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.048 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 143 average time/residue: 0.3735 time to fit residues: 69.6655 Evaluate side-chains 144 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1131 time to fit residues: 2.2327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1548 GLN C 112 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 13589 Z= 0.164 Angle : 0.501 5.418 19375 Z= 0.301 Chirality : 0.034 0.132 2173 Planarity : 0.004 0.047 1621 Dihedral : 28.903 147.688 3545 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.36 % 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: 0.13 (0.28), residues: 964 helix: 1.79 (0.23), residues: 532 sheet: -1.62 (0.95), residues: 28 loop : -2.27 (0.27), residues: 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.059 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 148 average time/residue: 0.3643 time to fit residues: 70.3150 Evaluate side-chains 144 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1119 time to fit residues: 1.7515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1599 ASN ** L1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 13589 Z= 0.214 Angle : 0.532 7.931 19375 Z= 0.315 Chirality : 0.035 0.129 2173 Planarity : 0.004 0.046 1621 Dihedral : 28.915 147.502 3545 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 964 helix: 1.80 (0.23), residues: 532 sheet: -1.67 (1.08), residues: 18 loop : -2.27 (0.27), residues: 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.175 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.3625 time to fit residues: 68.4766 Evaluate side-chains 140 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13589 Z= 0.183 Angle : 0.517 5.039 19375 Z= 0.310 Chirality : 0.035 0.130 2173 Planarity : 0.004 0.049 1621 Dihedral : 28.893 147.771 3545 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.48 % 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: 0.34 (0.28), residues: 964 helix: 1.95 (0.23), residues: 532 sheet: -1.47 (0.97), residues: 28 loop : -2.16 (0.28), residues: 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.140 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 139 average time/residue: 0.3865 time to fit residues: 70.1412 Evaluate side-chains 140 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2700 time to fit residues: 2.1343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.0170 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1548 GLN ** L1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1638 GLN A 68 GLN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 13589 Z= 0.317 Angle : 0.595 5.324 19375 Z= 0.348 Chirality : 0.038 0.133 2173 Planarity : 0.005 0.047 1621 Dihedral : 29.018 146.708 3545 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.12 % 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: -0.18 (0.27), residues: 964 helix: 1.48 (0.23), residues: 532 sheet: -1.80 (0.89), residues: 28 loop : -2.31 (0.27), residues: 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.517 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.3811 time to fit residues: 69.6263 Evaluate side-chains 139 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13589 Z= 0.190 Angle : 0.547 5.144 19375 Z= 0.326 Chirality : 0.036 0.133 2173 Planarity : 0.004 0.047 1621 Dihedral : 28.977 147.477 3545 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.12 % 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: 0.14 (0.27), residues: 964 helix: 1.75 (0.23), residues: 531 sheet: -1.66 (0.88), residues: 28 loop : -2.18 (0.28), residues: 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.147 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.3600 time to fit residues: 65.5364 Evaluate side-chains 139 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1078 time to fit residues: 1.3783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.184746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.141663 restraints weight = 14030.628| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.17 r_work: 0.3124 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 13589 Z= 0.297 Angle : 0.583 5.182 19375 Z= 0.343 Chirality : 0.038 0.130 2173 Planarity : 0.005 0.048 1621 Dihedral : 29.030 146.261 3545 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 0.12 % 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: -0.12 (0.27), residues: 964 helix: 1.52 (0.23), residues: 531 sheet: -1.53 (0.89), residues: 28 loop : -2.29 (0.27), residues: 405 =============================================================================== Job complete usr+sys time: 2267.13 seconds wall clock time: 41 minutes 52.00 seconds (2512.00 seconds total)