Starting phenix.real_space_refine on Sat Dec 9 17:54:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thu_41272/12_2023/8thu_41272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thu_41272/12_2023/8thu_41272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thu_41272/12_2023/8thu_41272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thu_41272/12_2023/8thu_41272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thu_41272/12_2023/8thu_41272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thu_41272/12_2023/8thu_41272.pdb" } resolution = 3.1 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= 0.004 sd= 0.029 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 P 291 5.49 5 S 12 5.16 5 C 6569 2.51 5 N 2223 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11902 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 773 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 6.81, per 1000 atoms: 0.57 Number of scatterers: 11902 At special positions: 0 Unit cell: (123.54, 124.392, 78.384, 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 12 16.00 P 291 15.00 O 2807 8.00 N 2223 7.00 C 6569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 71.2% alpha, 1.8% beta 144 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 5.56 Creating SS restraints... Processing helix chain 'G' and resid 8 through 13 removed outlier: 3.838A pdb=" N ALA G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.799A pdb=" N ALA G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 84 through 90 Processing helix chain 'C' and resid 8 through 13 removed outlier: 3.581A pdb=" N ALA C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 37 through 66 removed outlier: 3.819A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 3.513A pdb=" N LEU C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.771A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.727A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.062A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.619A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.559A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 36 removed outlier: 7.232A pdb=" N ARG G 35 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 93 through 94 removed outlier: 6.243A pdb=" N THR G 93 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.002A pdb=" N ARG C 35 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 94 removed outlier: 6.444A pdb=" N THR C 93 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.755A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 395 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2785 1.34 - 1.46: 4202 1.46 - 1.58: 5121 1.58 - 1.70: 580 1.70 - 1.82: 22 Bond restraints: 12710 Sorted by residual: bond pdb=" N VAL D 69 " pdb=" CA VAL D 69 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.51e+00 bond pdb=" N VAL H 69 " pdb=" CA VAL H 69 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.40e+00 bond pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.32e+00 bond pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.57e+00 bond pdb=" N ASN D 67 " pdb=" CA ASN D 67 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.56e+00 ... (remaining 12705 not shown) Histogram of bond angle deviations from ideal: 97.90 - 104.83: 1175 104.83 - 111.77: 6849 111.77 - 118.71: 3361 118.71 - 125.65: 6055 125.65 - 132.58: 988 Bond angle restraints: 18428 Sorted by residual: angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 127.36 -14.66 3.00e+00 1.11e-01 2.39e+01 angle pdb=" N GLY C 34 " pdb=" CA GLY C 34 " pdb=" C GLY C 34 " ideal model delta sigma weight residual 111.36 116.78 -5.42 1.17e+00 7.31e-01 2.14e+01 angle pdb=" CA LYS H 34 " pdb=" CB LYS H 34 " pdb=" CG LYS H 34 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" CA GLN C 11 " pdb=" CB GLN C 11 " pdb=" CG GLN C 11 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CB LYS C 91 " pdb=" CG LYS C 91 " pdb=" CD LYS C 91 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 ... (remaining 18423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 5372 34.71 - 69.43: 1478 69.43 - 104.14: 17 104.14 - 138.86: 1 138.86 - 173.57: 2 Dihedral angle restraints: 6870 sinusoidal: 4666 harmonic: 2204 Sorted by residual: dihedral pdb=" CA THR C 31 " pdb=" C THR C 31 " pdb=" N SER C 32 " pdb=" CA SER C 32 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C4' DC J 3 " pdb=" C3' DC J 3 " pdb=" O3' DC J 3 " pdb=" P DG J 4 " ideal model delta sinusoidal sigma weight residual -140.00 33.57 -173.57 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 134 " pdb=" C3' DT I 134 " pdb=" O3' DT I 134 " pdb=" P DA I 135 " ideal model delta sinusoidal sigma weight residual 220.00 51.93 168.07 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1535 0.034 - 0.069: 440 0.069 - 0.103: 108 0.103 - 0.137: 27 0.137 - 0.171: 4 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CA VAL H 69 " pdb=" N VAL H 69 " pdb=" C VAL H 69 " pdb=" CB VAL H 69 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA VAL D 69 " pdb=" N VAL D 69 " pdb=" C VAL D 69 " pdb=" CB VAL D 69 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" P DA I 135 " pdb=" OP1 DA I 135 " pdb=" OP2 DA I 135 " pdb=" O5' DA I 135 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 2111 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 81 " 0.263 9.50e-02 1.11e+02 1.18e-01 8.56e+00 pdb=" NE ARG C 81 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 81 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 81 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 81 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 87 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CG ASP G 87 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP G 87 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP G 87 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.03e+00 pdb=" N9 DG I 121 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.002 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 4 2.20 - 2.88: 3707 2.88 - 3.55: 16699 3.55 - 4.23: 31285 4.23 - 4.90: 47126 Nonbonded interactions: 98821 Sorted by model distance: nonbonded pdb=" NH1 ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 1.528 2.520 nonbonded pdb=" NH2 ARG B 92 " pdb=" CD2 LEU D 101 " model vdw 1.954 3.540 nonbonded pdb=" CZ ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 1.976 3.270 nonbonded pdb=" NH2 ARG G 29 " pdb=" OE1 GLU H 71 " model vdw 2.055 2.520 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.208 2.440 ... (remaining 98816 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 6 through 66 or (resid 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 108)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.010 Extract box with map and model: 6.670 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 39.240 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12710 Z= 0.228 Angle : 0.681 14.663 18428 Z= 0.401 Chirality : 0.036 0.171 2114 Planarity : 0.006 0.118 1317 Dihedral : 28.562 173.573 5446 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 18.48 % Favored : 81.52 % 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: 1.40 (0.30), residues: 744 helix: 2.07 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -2.14 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.029 0.002 TYR D 83 ARG 0.010 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3600 time to fit residues: 61.8230 Evaluate side-chains 115 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12710 Z= 0.243 Angle : 0.557 5.090 18428 Z= 0.339 Chirality : 0.034 0.127 2114 Planarity : 0.004 0.043 1317 Dihedral : 30.938 173.070 4024 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.43 % Allowed : 16.53 % Favored : 81.04 % 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: 2.27 (0.31), residues: 744 helix: 2.73 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -2.18 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.023 0.001 TYR D 83 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.982 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 134 average time/residue: 0.3331 time to fit residues: 58.7030 Evaluate side-chains 125 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1474 time to fit residues: 2.7916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8762 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12710 Z= 0.237 Angle : 0.546 5.000 18428 Z= 0.333 Chirality : 0.033 0.129 2114 Planarity : 0.004 0.040 1317 Dihedral : 30.862 174.266 4024 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.78 % Allowed : 17.34 % Favored : 80.88 % 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 (0.32), residues: 744 helix: 2.93 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.14 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.029 0.002 TYR D 83 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.985 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 132 average time/residue: 0.3375 time to fit residues: 58.7768 Evaluate side-chains 121 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1061 time to fit residues: 2.0125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS A 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12710 Z= 0.428 Angle : 0.624 7.630 18428 Z= 0.374 Chirality : 0.038 0.145 2114 Planarity : 0.005 0.039 1317 Dihedral : 31.218 173.501 4024 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.78 % Allowed : 17.50 % Favored : 80.71 % 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: 2.18 (0.32), residues: 744 helix: 2.71 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -2.36 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 33 PHE 0.011 0.001 PHE B 61 TYR 0.019 0.002 TYR D 83 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.940 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 121 average time/residue: 0.3477 time to fit residues: 55.0099 Evaluate side-chains 113 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1742 time to fit residues: 2.0082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.8791 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12710 Z= 0.287 Angle : 0.576 7.678 18428 Z= 0.348 Chirality : 0.034 0.141 2114 Planarity : 0.004 0.039 1317 Dihedral : 31.007 173.840 4024 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.78 % Allowed : 17.83 % Favored : 80.39 % 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: 2.36 (0.32), residues: 744 helix: 2.82 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.26 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 49 PHE 0.008 0.001 PHE F 61 TYR 0.014 0.001 TYR D 83 ARG 0.006 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.920 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 128 average time/residue: 0.3146 time to fit residues: 53.6910 Evaluate side-chains 118 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1072 time to fit residues: 1.7859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12710 Z= 0.309 Angle : 0.586 8.655 18428 Z= 0.352 Chirality : 0.035 0.141 2114 Planarity : 0.004 0.039 1317 Dihedral : 31.026 173.568 4024 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.97 % Allowed : 18.80 % Favored : 80.23 % 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: 2.34 (0.32), residues: 744 helix: 2.80 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.26 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.013 0.001 TYR D 83 ARG 0.004 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.920 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 120 average time/residue: 0.3234 time to fit residues: 51.3704 Evaluate side-chains 114 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2479 time to fit residues: 1.7505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12710 Z= 0.178 Angle : 0.544 9.202 18428 Z= 0.328 Chirality : 0.032 0.129 2114 Planarity : 0.004 0.039 1317 Dihedral : 30.622 174.372 4024 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.32 % Allowed : 20.42 % Favored : 79.25 % 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: 2.74 (0.32), residues: 744 helix: 3.08 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -2.02 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 113 PHE 0.007 0.001 PHE E 67 TYR 0.009 0.001 TYR D 83 ARG 0.004 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.948 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2980 time to fit residues: 53.1112 Evaluate side-chains 122 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12710 Z= 0.309 Angle : 0.593 9.237 18428 Z= 0.354 Chirality : 0.035 0.135 2114 Planarity : 0.004 0.037 1317 Dihedral : 30.915 173.883 4024 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.13 % Allowed : 20.58 % Favored : 78.28 % 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: 2.52 (0.32), residues: 744 helix: 2.91 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -2.12 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.016 0.002 TYR D 83 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.945 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 119 average time/residue: 0.3313 time to fit residues: 51.8352 Evaluate side-chains 118 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1120 time to fit residues: 2.0417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12710 Z= 0.199 Angle : 0.556 8.489 18428 Z= 0.334 Chirality : 0.033 0.137 2114 Planarity : 0.004 0.037 1317 Dihedral : 30.652 174.578 4024 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.16 % Allowed : 20.58 % Favored : 79.25 % 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: 2.73 (0.32), residues: 744 helix: 3.04 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE F 61 TYR 0.010 0.001 TYR D 83 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.988 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.3079 time to fit residues: 52.7881 Evaluate side-chains 122 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1041 time to fit residues: 1.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 overall best weight: 3.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12710 Z= 0.351 Angle : 0.611 7.985 18428 Z= 0.364 Chirality : 0.036 0.166 2114 Planarity : 0.004 0.035 1317 Dihedral : 31.019 173.786 4024 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.16 % Allowed : 21.56 % Favored : 78.28 % 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: 2.42 (0.32), residues: 744 helix: 2.82 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -2.13 (0.37), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.009 0.001 PHE B 61 TYR 0.024 0.002 TYR D 83 ARG 0.005 0.000 ARG D 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.847 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.3269 time to fit residues: 49.6610 Evaluate side-chains 111 residues out of total 634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.0070 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.039399 restraints weight = 50814.776| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.91 r_work: 0.2658 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12710 Z= 0.198 Angle : 0.559 7.998 18428 Z= 0.335 Chirality : 0.033 0.139 2114 Planarity : 0.004 0.037 1317 Dihedral : 30.701 174.433 4024 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.16 % Allowed : 21.72 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.32), residues: 744 helix: 2.98 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 113 PHE 0.006 0.001 PHE F 61 TYR 0.011 0.001 TYR D 83 ARG 0.004 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.17 seconds wall clock time: 39 minutes 28.92 seconds (2368.92 seconds total)