Starting phenix.real_space_refine on Sun Dec 10 01:23:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/12_2023/6s01_10069_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/12_2023/6s01_10069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/12_2023/6s01_10069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/12_2023/6s01_10069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/12_2023/6s01_10069_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/12_2023/6s01_10069_updated.pdb" } resolution = 3.2 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= 0.007 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 300 5.49 5 S 13 5.16 5 C 7231 2.51 5 N 2421 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 57": "OD1" <-> "OD2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K ARG 74": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12959 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 7.43, per 1000 atoms: 0.57 Number of scatterers: 12959 At special positions: 0 Unit cell: (90.3, 120.75, 135.45, 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 13 16.00 P 300 15.00 O 2994 8.00 N 2421 7.00 C 7231 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: 6.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 2 sheets defined 55.2% alpha, 1.4% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 7.88 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.521A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.789A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.542A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.734A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.966A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.621A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.683A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.544A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.943A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.957A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.734A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 86 removed outlier: 5.137A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 42 through 44 removed outlier: 3.538A pdb=" N PHE K 44 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 6.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2251 1.33 - 1.45: 4697 1.45 - 1.57: 6242 1.57 - 1.69: 598 1.69 - 1.81: 26 Bond restraints: 13814 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.756 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.762 0.055 2.00e-02 2.50e+03 7.53e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.498 -0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.52e+00 ... (remaining 13809 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.57: 1509 105.57 - 112.66: 7652 112.66 - 119.75: 4623 119.75 - 126.84: 5303 126.84 - 133.92: 856 Bond angle restraints: 19943 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 120.20 125.90 -5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.12 -5.51 1.56e+00 4.11e-01 1.25e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 125.04 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 120.20 124.93 -4.73 1.50e+00 4.44e-01 9.96e+00 angle pdb=" CA GLU K 63 " pdb=" CB GLU K 63 " pdb=" CG GLU K 63 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.66e+00 ... (remaining 19938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6150 34.28 - 68.56: 1377 68.56 - 102.84: 15 102.84 - 137.12: 2 137.12 - 171.40: 1 Dihedral angle restraints: 7545 sinusoidal: 5071 harmonic: 2474 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.07 19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.60 171.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1250 0.035 - 0.071: 810 0.071 - 0.106: 147 0.106 - 0.142: 38 0.142 - 0.177: 8 Chirality restraints: 2253 Sorted by residual: chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2250 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO E 66 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO C 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO G 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.037 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3133 2.81 - 3.33: 10202 3.33 - 3.85: 23968 3.85 - 4.38: 31467 4.38 - 4.90: 43638 Nonbonded interactions: 112408 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.284 2.440 nonbonded pdb=" NH2 ARG H 83 " pdb=" OP2 DG J -33 " model vdw 2.331 2.520 nonbonded pdb=" NH2 ARG D 83 " pdb=" OP2 DA I -33 " model vdw 2.361 2.520 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.361 2.520 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.364 2.520 ... (remaining 112403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.020 Extract box with map and model: 4.210 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 42.880 Find NCS groups from input model: 0.490 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.008 0.076 13814 Z= 0.470 Angle : 0.723 7.969 19943 Z= 0.427 Chirality : 0.044 0.177 2253 Planarity : 0.006 0.069 1485 Dihedral : 26.197 171.395 5947 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 7.99 % Favored : 90.18 % 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: -5.85 (0.18), residues: 831 helix: -4.46 (0.09), residues: 530 sheet: -4.09 (0.99), residues: 17 loop : -2.11 (0.29), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 82 HIS 0.004 0.001 HIS G 31 PHE 0.013 0.002 PHE K 45 TYR 0.012 0.002 TYR B 72 ARG 0.004 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.080 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 206 average time/residue: 0.3656 time to fit residues: 97.8861 Evaluate side-chains 150 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1166 time to fit residues: 2.6070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS E 68 GLN E 76 GLN F 18 HIS F 25 ASN F 75 HIS ** K 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13814 Z= 0.198 Angle : 0.577 5.597 19943 Z= 0.351 Chirality : 0.035 0.140 2253 Planarity : 0.005 0.054 1485 Dihedral : 29.872 155.572 4233 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.68 % Allowed : 11.92 % Favored : 86.40 % 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: -2.79 (0.24), residues: 831 helix: -1.84 (0.19), residues: 524 sheet: -3.78 (1.03), residues: 17 loop : -1.36 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.010 0.001 HIS K 20 PHE 0.017 0.002 PHE K 45 TYR 0.018 0.001 TYR K 61 ARG 0.005 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.101 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 165 average time/residue: 0.3334 time to fit residues: 72.9839 Evaluate side-chains 148 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1734 time to fit residues: 2.9901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13814 Z= 0.319 Angle : 0.607 5.782 19943 Z= 0.359 Chirality : 0.038 0.137 2253 Planarity : 0.005 0.046 1485 Dihedral : 30.187 151.459 4233 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.10 % Allowed : 12.76 % Favored : 85.13 % 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: -1.34 (0.27), residues: 831 helix: -0.46 (0.22), residues: 532 sheet: -3.17 (1.06), residues: 18 loop : -1.33 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.015 0.002 PHE K 45 TYR 0.014 0.002 TYR B 51 ARG 0.005 0.001 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.055 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 0.3190 time to fit residues: 65.8139 Evaluate side-chains 143 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1771 time to fit residues: 5.1991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13814 Z= 0.273 Angle : 0.570 5.500 19943 Z= 0.340 Chirality : 0.036 0.145 2253 Planarity : 0.004 0.046 1485 Dihedral : 30.150 147.853 4233 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.26 % Allowed : 14.73 % Favored : 84.01 % 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: -0.50 (0.29), residues: 831 helix: 0.26 (0.23), residues: 533 sheet: -2.96 (1.12), residues: 18 loop : -1.13 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 82 HIS 0.003 0.001 HIS E 113 PHE 0.020 0.002 PHE K 59 TYR 0.012 0.001 TYR B 51 ARG 0.003 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.113 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 145 average time/residue: 0.3353 time to fit residues: 65.2174 Evaluate side-chains 143 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1694 time to fit residues: 3.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13814 Z= 0.235 Angle : 0.558 5.752 19943 Z= 0.335 Chirality : 0.035 0.156 2253 Planarity : 0.004 0.042 1485 Dihedral : 30.149 147.632 4233 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.70 % Allowed : 16.27 % Favored : 83.03 % 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: -0.09 (0.29), residues: 831 helix: 0.58 (0.23), residues: 532 sheet: -2.86 (1.14), residues: 18 loop : -0.98 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 82 HIS 0.006 0.001 HIS K 20 PHE 0.021 0.002 PHE K 59 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.096 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 140 average time/residue: 0.3420 time to fit residues: 64.0382 Evaluate side-chains 140 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1264 time to fit residues: 1.9623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13814 Z= 0.259 Angle : 0.564 5.926 19943 Z= 0.336 Chirality : 0.036 0.151 2253 Planarity : 0.004 0.043 1485 Dihedral : 30.167 144.615 4233 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.84 % Allowed : 16.55 % Favored : 82.61 % 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: 0.22 (0.29), residues: 831 helix: 0.85 (0.23), residues: 527 sheet: -2.80 (1.18), residues: 18 loop : -0.87 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 82 HIS 0.003 0.001 HIS K 20 PHE 0.018 0.002 PHE K 59 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.103 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 144 average time/residue: 0.3321 time to fit residues: 64.3602 Evaluate side-chains 143 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1219 time to fit residues: 1.8573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13814 Z= 0.193 Angle : 0.556 12.851 19943 Z= 0.331 Chirality : 0.034 0.160 2253 Planarity : 0.004 0.042 1485 Dihedral : 30.162 144.993 4233 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.56 % Allowed : 18.09 % Favored : 81.35 % 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: 0.44 (0.29), residues: 831 helix: 1.02 (0.23), residues: 532 sheet: -2.75 (1.18), residues: 18 loop : -0.80 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 82 HIS 0.003 0.001 HIS K 20 PHE 0.017 0.001 PHE K 59 TYR 0.009 0.001 TYR B 51 ARG 0.008 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.088 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 142 average time/residue: 0.3161 time to fit residues: 61.0303 Evaluate side-chains 143 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3361 time to fit residues: 2.6295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13814 Z= 0.238 Angle : 0.557 12.009 19943 Z= 0.331 Chirality : 0.035 0.157 2253 Planarity : 0.004 0.045 1485 Dihedral : 30.120 143.536 4233 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.70 % Allowed : 17.81 % Favored : 81.49 % 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: 0.56 (0.29), residues: 831 helix: 1.11 (0.23), residues: 532 sheet: -2.60 (1.20), residues: 18 loop : -0.76 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP K 82 HIS 0.003 0.001 HIS K 20 PHE 0.019 0.002 PHE K 59 TYR 0.009 0.001 TYR B 51 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 1.021 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 144 average time/residue: 0.3238 time to fit residues: 63.2811 Evaluate side-chains 145 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1209 time to fit residues: 2.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13814 Z= 0.398 Angle : 0.643 11.976 19943 Z= 0.371 Chirality : 0.041 0.163 2253 Planarity : 0.005 0.044 1485 Dihedral : 30.379 141.728 4233 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.28 % Allowed : 17.95 % Favored : 81.77 % 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: 0.17 (0.29), residues: 831 helix: 0.80 (0.23), residues: 524 sheet: -1.99 (1.37), residues: 18 loop : -0.92 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.020 0.002 PHE K 59 TYR 0.011 0.002 TYR B 51 ARG 0.005 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.045 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.3249 time to fit residues: 62.2871 Evaluate side-chains 138 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1144 time to fit residues: 1.4684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.0970 chunk 73 optimal weight: 10.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 44 GLN F 27 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13814 Z= 0.194 Angle : 0.567 12.738 19943 Z= 0.338 Chirality : 0.035 0.171 2253 Planarity : 0.004 0.045 1485 Dihedral : 30.345 143.603 4233 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.28 % Allowed : 18.79 % Favored : 80.93 % 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: 0.54 (0.29), residues: 831 helix: 1.06 (0.23), residues: 526 sheet: -2.11 (1.35), residues: 18 loop : -0.69 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP K 82 HIS 0.003 0.001 HIS K 20 PHE 0.019 0.001 PHE K 59 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.027 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.3188 time to fit residues: 60.0836 Evaluate side-chains 136 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1116 time to fit residues: 1.4123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 0.0270 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 44 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104042 restraints weight = 20031.098| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 0.97 r_work: 0.3202 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13814 Z= 0.161 Angle : 0.560 12.735 19943 Z= 0.333 Chirality : 0.034 0.189 2253 Planarity : 0.004 0.044 1485 Dihedral : 30.298 144.160 4233 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.14 % Allowed : 18.65 % Favored : 81.21 % 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: 0.90 (0.30), residues: 831 helix: 1.35 (0.23), residues: 526 sheet: -2.20 (1.32), residues: 18 loop : -0.54 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP K 82 HIS 0.004 0.001 HIS B 75 PHE 0.021 0.002 PHE K 59 TYR 0.009 0.001 TYR B 51 ARG 0.003 0.000 ARG E 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2588.04 seconds wall clock time: 47 minutes 37.30 seconds (2857.30 seconds total)