Starting phenix.real_space_refine (version: dev) on Tue Apr 5 16:18:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/04_2022/6n2p_9332.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/04_2022/6n2p_9332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/04_2022/6n2p_9332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/04_2022/6n2p_9332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/04_2022/6n2p_9332.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/04_2022/6n2p_9332.pdb" } resolution = 4.0 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= -0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 14570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "B" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "C" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "D" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "E" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "G" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "H" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "I" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "J" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Time building chain proxies: 7.13, per 1000 atoms: 0.49 Number of scatterers: 14570 At special positions: 0 Unit cell: (91.14, 91.14, 87.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1330 8.00 N 1210 7.00 C 4630 6.00 H 7380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Proline residue: B 32 - end of helix Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 57 through 70 removed outlier: 3.658A pdb=" N VAL C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 57 through 70 removed outlier: 3.658A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 87 through 95 Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 18 through 25 Processing helix chain 'E' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Proline residue: E 32 - end of helix Processing helix chain 'E' and resid 41 through 50 Processing helix chain 'E' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 87 Processing helix chain 'E' and resid 87 through 95 Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Proline residue: F 32 - end of helix Processing helix chain 'F' and resid 41 through 50 Processing helix chain 'F' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 87 through 95 Processing helix chain 'G' and resid 10 through 15 Processing helix chain 'G' and resid 18 through 25 Processing helix chain 'G' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 41 through 50 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 Processing helix chain 'G' and resid 87 through 95 Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 18 through 25 Processing helix chain 'H' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 41 through 50 Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 87 Processing helix chain 'H' and resid 87 through 95 Processing helix chain 'I' and resid 10 through 15 Processing helix chain 'I' and resid 18 through 25 Processing helix chain 'I' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE I 30 " --> pdb=" O ASP I 26 " (cutoff:3.500A) Proline residue: I 32 - end of helix Processing helix chain 'I' and resid 41 through 50 Processing helix chain 'I' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 87 Processing helix chain 'I' and resid 87 through 95 Processing helix chain 'J' and resid 10 through 15 Processing helix chain 'J' and resid 18 through 25 Processing helix chain 'J' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE J 30 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Proline residue: J 32 - end of helix Processing helix chain 'J' and resid 41 through 50 Processing helix chain 'J' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 87 Processing helix chain 'J' and resid 87 through 95 420 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 13.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7360 1.03 - 1.23: 20 1.23 - 1.42: 2950 1.42 - 1.62: 4360 1.62 - 1.81: 20 Bond restraints: 14710 Sorted by residual: bond pdb=" CG LEU H 65 " pdb=" CD1 LEU H 65 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU J 65 " pdb=" CD1 LEU J 65 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU G 65 " pdb=" CD1 LEU G 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LEU E 65 " pdb=" CD1 LEU E 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LEU I 65 " pdb=" CD1 LEU I 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 14705 not shown) Histogram of bond angle deviations from ideal: 102.31 - 108.64: 5789 108.64 - 114.96: 13182 114.96 - 121.28: 5256 121.28 - 127.61: 2453 127.61 - 133.93: 60 Bond angle restraints: 26740 Sorted by residual: angle pdb=" C GLN C 36 " pdb=" N CYS C 37 " pdb=" CA CYS C 37 " ideal model delta sigma weight residual 122.31 116.66 5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" C GLN F 36 " pdb=" N CYS F 37 " pdb=" CA CYS F 37 " ideal model delta sigma weight residual 122.31 116.66 5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" C GLN E 36 " pdb=" N CYS E 37 " pdb=" CA CYS E 37 " ideal model delta sigma weight residual 122.31 116.67 5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" C GLN A 36 " pdb=" N CYS A 37 " pdb=" CA CYS A 37 " ideal model delta sigma weight residual 122.31 116.67 5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" C GLN B 36 " pdb=" N CYS B 37 " pdb=" CA CYS B 37 " ideal model delta sigma weight residual 122.31 116.69 5.62 2.00e+00 2.50e-01 7.91e+00 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.17: 5171 7.17 - 14.34: 529 14.34 - 21.52: 110 21.52 - 28.69: 40 28.69 - 35.86: 40 Dihedral angle restraints: 5890 sinusoidal: 2900 harmonic: 2990 Sorted by residual: dihedral pdb=" CA LEU E 54 " pdb=" C LEU E 54 " pdb=" N VAL E 55 " pdb=" CA VAL E 55 " ideal model delta harmonic sigma weight residual -180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LEU F 54 " pdb=" C LEU F 54 " pdb=" N VAL F 55 " pdb=" CA VAL F 55 " ideal model delta harmonic sigma weight residual -180.00 -163.95 -16.05 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA LEU J 54 " pdb=" C LEU J 54 " pdb=" N VAL J 55 " pdb=" CA VAL J 55 " ideal model delta harmonic sigma weight residual -180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 5887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 529 0.025 - 0.050: 353 0.050 - 0.075: 192 0.075 - 0.100: 46 0.100 - 0.125: 40 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA PRO J 32 " pdb=" N PRO J 32 " pdb=" C PRO J 32 " pdb=" CB PRO J 32 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA PRO C 52 " pdb=" N PRO C 52 " pdb=" C PRO C 52 " pdb=" CB PRO C 52 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1157 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 51 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 51 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO D 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 51 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO I 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO I 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 52 " -0.030 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 817 2.19 - 2.79: 30538 2.79 - 3.39: 36506 3.39 - 4.00: 45180 4.00 - 4.60: 72363 Nonbonded interactions: 185404 Sorted by model distance: nonbonded pdb="HD22 ASN D 53 " pdb=" O PRO E 52 " model vdw 1.586 1.850 nonbonded pdb=" OE2 GLU B 15 " pdb=" HE ARG E 35 " model vdw 1.589 1.850 nonbonded pdb=" OE2 GLU C 15 " pdb=" HE ARG F 35 " model vdw 1.596 1.850 nonbonded pdb=" HE ARG B 35 " pdb=" OE2 GLU H 15 " model vdw 1.601 1.850 nonbonded pdb="HD22 ASN E 53 " pdb=" O PRO F 52 " model vdw 1.621 1.850 ... (remaining 185399 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 4630 2.51 5 N 1210 2.21 5 O 1330 1.98 5 H 7380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.980 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: 0.250 Extract box with map and model: 7.080 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 48.140 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.009 0.046 7330 Z= 0.615 Angle : 0.872 6.337 9950 Z= 0.466 Chirality : 0.043 0.125 1160 Planarity : 0.007 0.055 1250 Dihedral : 7.864 35.860 2810 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % 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: -4.67 (0.22), residues: 860 helix: -2.30 (0.16), residues: 670 sheet: None (None), residues: 0 loop : -5.46 (0.22), residues: 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.6438 time to fit residues: 91.4317 Evaluate side-chains 56 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.7335 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 7330 Z= 0.222 Angle : 0.615 4.922 9950 Z= 0.324 Chirality : 0.036 0.103 1160 Planarity : 0.006 0.040 1250 Dihedral : 5.056 14.953 980 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer Outliers : 1.08 % 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: -2.53 (0.27), residues: 860 helix: -0.55 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -5.69 (0.21), residues: 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 0.4142 time to fit residues: 38.5349 Evaluate side-chains 46 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1670 time to fit residues: 2.9037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- 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: 0.7467 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 7330 Z= 0.344 Angle : 0.643 4.976 9950 Z= 0.345 Chirality : 0.035 0.103 1160 Planarity : 0.005 0.030 1250 Dihedral : 4.946 14.778 980 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer Outliers : 0.84 % 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: -2.06 (0.28), residues: 860 helix: -0.25 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -5.66 (0.23), residues: 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.4023 time to fit residues: 21.7640 Evaluate side-chains 33 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1620 time to fit residues: 3.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.0470 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 overall best weight: 2.9484 ------------------------------------------------------------------------------- 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: 0.7414 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 7330 Z= 0.171 Angle : 0.544 4.967 9950 Z= 0.279 Chirality : 0.035 0.104 1160 Planarity : 0.004 0.026 1250 Dihedral : 4.498 14.983 980 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % 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: -1.05 (0.29), residues: 860 helix: 0.46 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -5.28 (0.24), residues: 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.3703 time to fit residues: 18.5156 Evaluate side-chains 23 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 overall best weight: 3.7384 ------------------------------------------------------------------------------- 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: 0.7442 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 7330 Z= 0.202 Angle : 0.545 4.881 9950 Z= 0.283 Chirality : 0.035 0.106 1160 Planarity : 0.004 0.026 1250 Dihedral : 4.466 14.660 980 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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: -0.63 (0.29), residues: 860 helix: 0.73 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.98 (0.27), residues: 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.4010 time to fit residues: 14.8928 Evaluate side-chains 21 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 1.351 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1490 time to fit residues: 2.2244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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: 0.7469 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 7330 Z= 0.224 Angle : 0.555 4.684 9950 Z= 0.288 Chirality : 0.035 0.108 1160 Planarity : 0.004 0.023 1250 Dihedral : 4.510 15.028 980 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % 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: -0.48 (0.29), residues: 860 helix: 0.72 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -4.76 (0.31), residues: 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.3747 time to fit residues: 14.1530 Evaluate side-chains 20 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2320 time to fit residues: 2.8443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.7511 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 7330 Z= 0.285 Angle : 0.588 4.670 9950 Z= 0.312 Chirality : 0.035 0.110 1160 Planarity : 0.004 0.029 1250 Dihedral : 4.726 15.221 980 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % 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: -0.72 (0.29), residues: 860 helix: 0.61 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.78 (0.29), residues: 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.4576 time to fit residues: 11.5080 Evaluate side-chains 12 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.7441 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 7330 Z= 0.147 Angle : 0.524 4.753 9950 Z= 0.269 Chirality : 0.035 0.107 1160 Planarity : 0.003 0.024 1250 Dihedral : 4.355 15.089 980 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: 0.06 (0.30), residues: 860 helix: 1.16 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -4.51 (0.30), residues: 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2725 time to fit residues: 10.3846 Evaluate side-chains 13 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.7494 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.021 7330 Z= 0.234 Angle : 0.556 4.646 9950 Z= 0.293 Chirality : 0.035 0.116 1160 Planarity : 0.004 0.038 1250 Dihedral : 4.558 15.169 980 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % 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: -0.20 (0.29), residues: 860 helix: 0.97 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.56 (0.30), residues: 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.2826 time to fit residues: 7.9097 Evaluate side-chains 13 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0070 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7804 ------------------------------------------------------------------------------- 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: 0.7438 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 7330 Z= 0.145 Angle : 0.532 5.471 9950 Z= 0.274 Chirality : 0.035 0.107 1160 Planarity : 0.003 0.030 1250 Dihedral : 4.305 15.085 980 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: 0.26 (0.30), residues: 860 helix: 1.28 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -4.32 (0.31), residues: 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.2622 time to fit residues: 7.8784 Evaluate side-chains 14 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.051360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047727 restraints weight = 264469.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048664 restraints weight = 108036.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049208 restraints weight = 60187.853| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 7330 Z= 0.149 Angle : 0.522 4.765 9950 Z= 0.269 Chirality : 0.035 0.135 1160 Planarity : 0.003 0.037 1250 Dihedral : 4.248 14.999 980 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % 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: 0.39 (0.30), residues: 860 helix: 1.37 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -4.27 (0.32), residues: 180 =============================================================================== Job complete usr+sys time: 2253.87 seconds wall clock time: 41 minutes 1.53 seconds (2461.53 seconds total)