Starting phenix.real_space_refine on Sat Mar 16 11:09:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/03_2024/6n2p_9332.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/03_2024/6n2p_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_9332/03_2024/6n2p_9332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/03_2024/6n2p_9332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/03_2024/6n2p_9332.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2p_9332/03_2024/6n2p_9332.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-5265/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: 6.33, per 1000 atoms: 0.43 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: 10.64 Conformation dependent library (CDL) restraints added in 1.5 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: 1.09 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: 4.65 Time building geometry restraints manager: 11.18 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 - 11.88: 6381 11.88 - 23.77: 259 23.77 - 35.65: 100 35.65 - 47.53: 70 47.53 - 59.41: 30 Dihedral angle restraints: 6840 sinusoidal: 3850 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 6837 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 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: 2.040 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: 0.210 Extract box with map and model: 6.220 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 44.720 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 % Allowed : 3.61 % Favored : 96.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 11 HIS 0.004 0.003 HIS G 73 PHE 0.013 0.004 PHE J 79 TYR 0.004 0.001 TYR D 87 ARG 0.003 0.001 ARG I 18 *********************** 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 : 1.242 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: 0.7443 time to fit residues: 103.6035 Evaluate side-chains 56 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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: 0.0000 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7330 Z= 0.196 Angle : 0.602 4.794 9950 Z= 0.316 Chirality : 0.036 0.101 1160 Planarity : 0.006 0.044 1250 Dihedral : 5.000 14.715 980 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.72 % Allowed : 7.35 % Favored : 91.93 % 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: -2.41 (0.27), residues: 860 helix: -0.46 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -5.67 (0.21), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 11 HIS 0.001 0.000 HIS C 73 PHE 0.006 0.001 PHE E 17 TYR 0.011 0.001 TYR F 87 ARG 0.004 0.001 ARG E 35 *********************** 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 70 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 1.311 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 outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 0.4354 time to fit residues: 38.9995 Evaluate side-chains 47 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain I residue 12 SER 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: 9.9990 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- 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: 0.7716 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7330 Z= 0.281 Angle : 0.588 4.700 9950 Z= 0.314 Chirality : 0.035 0.101 1160 Planarity : 0.005 0.034 1250 Dihedral : 4.710 14.424 980 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.84 % Allowed : 7.83 % Favored : 91.33 % 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: -1.64 (0.28), residues: 860 helix: 0.08 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -5.68 (0.23), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 11 HIS 0.001 0.000 HIS F 73 PHE 0.003 0.001 PHE E 17 TYR 0.008 0.001 TYR D 87 ARG 0.004 0.001 ARG B 35 *********************** 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 43 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 1.678 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 outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.4650 time to fit residues: 26.7618 Evaluate side-chains 36 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain I residue 44 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 64 optimal weight: 0.1980 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7330 Z= 0.216 Angle : 0.558 4.790 9950 Z= 0.292 Chirality : 0.035 0.124 1160 Planarity : 0.004 0.029 1250 Dihedral : 4.562 15.014 980 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.48 % Allowed : 8.43 % Favored : 91.08 % 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: -0.93 (0.29), residues: 860 helix: 0.60 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -5.18 (0.23), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 11 HIS 0.001 0.000 HIS B 73 PHE 0.003 0.001 PHE H 17 TYR 0.009 0.001 TYR J 87 ARG 0.005 0.001 ARG E 35 *********************** 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 34 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 1.142 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: 4 outliers final: 3 residues processed: 33 average time/residue: 0.3640 time to fit residues: 18.0647 Evaluate side-chains 25 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 overall best weight: 6.3188 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7330 Z= 0.311 Angle : 0.606 4.649 9950 Z= 0.325 Chirality : 0.035 0.117 1160 Planarity : 0.005 0.027 1250 Dihedral : 4.855 15.456 980 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 1.08 % Allowed : 8.07 % Favored : 90.84 % 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: -1.16 (0.28), residues: 860 helix: 0.32 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -5.05 (0.26), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 11 HIS 0.002 0.001 HIS J 73 PHE 0.004 0.001 PHE G 17 TYR 0.010 0.001 TYR D 87 ARG 0.005 0.001 ARG B 35 *********************** 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 27 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 18 time to evaluate : 1.406 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 outliers start: 9 outliers final: 9 residues processed: 26 average time/residue: 0.3515 time to fit residues: 14.7181 Evaluate side-chains 24 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 15 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 44 ASP 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: 1.9990 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.7786 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7330 Z= 0.195 Angle : 0.540 4.691 9950 Z= 0.281 Chirality : 0.035 0.108 1160 Planarity : 0.003 0.029 1250 Dihedral : 4.563 15.360 980 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.72 % Allowed : 8.55 % Favored : 90.72 % 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: -0.51 (0.29), residues: 860 helix: 0.75 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.67 (0.29), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 11 HIS 0.001 0.000 HIS D 73 PHE 0.002 0.000 PHE G 17 TYR 0.006 0.001 TYR I 87 ARG 0.003 0.000 ARG A 35 *********************** 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 25 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 25 average time/residue: 0.3560 time to fit residues: 14.4011 Evaluate side-chains 19 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 44 ASP 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: 8.9990 chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 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: 0.7836 moved from start: 0.5368 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= 0.287 Angle : 0.585 4.561 9950 Z= 0.313 Chirality : 0.035 0.109 1160 Planarity : 0.004 0.029 1250 Dihedral : 4.828 15.529 980 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.96 % Allowed : 8.31 % Favored : 90.72 % 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: -0.72 (0.29), residues: 860 helix: 0.57 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.60 (0.30), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 11 HIS 0.002 0.001 HIS J 73 PHE 0.004 0.001 PHE C 79 TYR 0.009 0.001 TYR I 87 ARG 0.004 0.000 ARG J 35 *********************** 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 21 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 13 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 20 average time/residue: 0.3024 time to fit residues: 10.4901 Evaluate side-chains 18 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 10 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 44 ASP 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: 1.9990 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7330 Z= 0.218 Angle : 0.549 4.556 9950 Z= 0.289 Chirality : 0.035 0.108 1160 Planarity : 0.003 0.027 1250 Dihedral : 4.667 15.783 980 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.84 % Allowed : 8.67 % Favored : 90.48 % 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: -0.35 (0.29), residues: 860 helix: 0.81 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.39 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 11 HIS 0.001 0.000 HIS J 73 PHE 0.003 0.001 PHE G 17 TYR 0.007 0.001 TYR I 87 ARG 0.003 0.000 ARG J 35 *********************** 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 17 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 10 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 17 average time/residue: 0.2449 time to fit residues: 8.3915 Evaluate side-chains 14 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 7 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain H residue 44 ASP Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 0.0980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 7330 Z= 0.135 Angle : 0.512 4.561 9950 Z= 0.264 Chirality : 0.035 0.108 1160 Planarity : 0.003 0.029 1250 Dihedral : 4.383 15.413 980 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.60 % Allowed : 9.04 % Favored : 90.36 % 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: 0.27 (0.30), residues: 860 helix: 1.24 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -4.12 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 11 HIS 0.001 0.000 HIS H 73 PHE 0.003 0.000 PHE F 17 TYR 0.005 0.001 TYR D 86 ARG 0.002 0.000 ARG J 35 *********************** 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 19 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 14 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 53 ASN cc_start: 0.7968 (m-40) cc_final: 0.7761 (m110) REVERT: E 53 ASN cc_start: 0.8164 (m-40) cc_final: 0.7862 (m-40) outliers start: 5 outliers final: 4 residues processed: 19 average time/residue: 0.2411 time to fit residues: 9.1730 Evaluate side-chains 14 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain I residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7330 Z= 0.166 Angle : 0.517 4.486 9950 Z= 0.269 Chirality : 0.035 0.120 1160 Planarity : 0.003 0.028 1250 Dihedral : 4.446 15.462 980 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.48 % Allowed : 9.52 % Favored : 90.00 % 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: 0.30 (0.29), residues: 860 helix: 1.26 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -4.08 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 11 HIS 0.001 0.000 HIS J 73 PHE 0.003 0.000 PHE H 17 TYR 0.005 0.001 TYR I 87 ARG 0.003 0.000 ARG J 35 ********************** 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: 4 poor density : 11 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 53 ASN cc_start: 0.8040 (m-40) cc_final: 0.7826 (m110) REVERT: E 53 ASN cc_start: 0.8276 (m-40) cc_final: 0.7974 (m-40) outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.2063 time to fit residues: 6.6121 Evaluate side-chains 15 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 11 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain I residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.050580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046903 restraints weight = 268037.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047877 restraints weight = 113036.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.048417 restraints weight = 62488.955| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7330 Z= 0.172 Angle : 0.519 4.486 9950 Z= 0.270 Chirality : 0.035 0.105 1160 Planarity : 0.003 0.025 1250 Dihedral : 4.474 15.486 980 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.60 % Allowed : 9.40 % Favored : 90.00 % 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 (0.29), residues: 860 helix: 1.32 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.05 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 11 HIS 0.001 0.000 HIS J 73 PHE 0.003 0.001 PHE H 17 TYR 0.005 0.001 TYR I 87 ARG 0.003 0.000 ARG J 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2279.26 seconds wall clock time: 41 minutes 6.67 seconds (2466.67 seconds total)