Starting phenix.real_space_refine on Thu Mar 14 19:35:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/03_2024/7xqi_33397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/03_2024/7xqi_33397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/03_2024/7xqi_33397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/03_2024/7xqi_33397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/03_2024/7xqi_33397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/03_2024/7xqi_33397.pdb" } resolution = 3.7 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6396 2.51 5 N 1518 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "D" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Time building chain proxies: 5.21, per 1000 atoms: 0.54 Number of scatterers: 9582 At special positions: 0 Unit cell: (102.608, 106, 103.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1620 8.00 N 1518 7.00 C 6396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 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: 3.64 Conformation dependent library (CDL) restraints added in 1.9 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 74.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.802A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 177 Processing helix chain 'A' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 86 through 112 removed outlier: 3.728A pdb=" N GLU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 177 Processing helix chain 'B' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.802A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 86 through 112 removed outlier: 3.726A pdb=" N GLU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 177 Processing helix chain 'C' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 19 through 31 Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.704A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 177 Processing helix chain 'D' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'E' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 177 Processing helix chain 'E' and resid 204 through 233 removed outlier: 3.597A pdb=" N ILE E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 233 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.523A pdb=" N GLY F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.704A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 177 Processing helix chain 'F' and resid 204 through 233 removed outlier: 3.597A pdb=" N ILE F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.516A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.516A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2826 1.34 - 1.46: 2233 1.46 - 1.58: 4703 1.58 - 1.69: 6 1.69 - 1.81: 60 Bond restraints: 9828 Sorted by residual: bond pdb=" CA TYR E 17 " pdb=" CB TYR E 17 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.85e+00 bond pdb=" CA TYR F 17 " pdb=" CB TYR F 17 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.83e+00 bond pdb=" CA TYR B 17 " pdb=" CB TYR B 17 " ideal model delta sigma weight residual 1.531 1.599 -0.068 3.12e-02 1.03e+03 4.76e+00 bond pdb=" CA TYR A 17 " pdb=" CB TYR A 17 " ideal model delta sigma weight residual 1.531 1.599 -0.068 3.12e-02 1.03e+03 4.75e+00 bond pdb=" CA TYR C 17 " pdb=" CB TYR C 17 " ideal model delta sigma weight residual 1.531 1.598 -0.068 3.12e-02 1.03e+03 4.72e+00 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.97: 192 106.97 - 113.73: 5527 113.73 - 120.50: 4222 120.50 - 127.26: 3259 127.26 - 134.03: 108 Bond angle restraints: 13308 Sorted by residual: angle pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta sigma weight residual 121.19 127.65 -6.46 1.59e+00 3.96e-01 1.65e+01 angle pdb=" C PRO F 193 " pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta sigma weight residual 121.19 127.65 -6.46 1.59e+00 3.96e-01 1.65e+01 angle pdb=" C PRO D 193 " pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 angle pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 angle pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 ... (remaining 13303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 5088 14.30 - 28.60: 450 28.60 - 42.89: 168 42.89 - 57.19: 42 57.19 - 71.49: 36 Dihedral angle restraints: 5784 sinusoidal: 2334 harmonic: 3450 Sorted by residual: dihedral pdb=" CA PRO C 193 " pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PRO F 193 " pdb=" C PRO F 193 " pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO E 193 " pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 793 0.028 - 0.056: 469 0.056 - 0.084: 182 0.084 - 0.113: 46 0.113 - 0.141: 34 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA ARG C 202 " pdb=" N ARG C 202 " pdb=" C ARG C 202 " pdb=" CB ARG C 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ARG F 202 " pdb=" N ARG F 202 " pdb=" C ARG F 202 " pdb=" CB ARG F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA VAL B 14 " pdb=" N VAL B 14 " pdb=" C VAL B 14 " pdb=" CB VAL B 14 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1521 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 167 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL C 167 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL C 167 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 168 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 167 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C VAL D 167 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL D 167 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA D 168 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 167 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C VAL A 167 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL A 167 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 168 " 0.009 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2913 2.82 - 3.34: 8342 3.34 - 3.86: 15540 3.86 - 4.38: 14891 4.38 - 4.90: 27616 Nonbonded interactions: 69302 Sorted by model distance: nonbonded pdb=" O ILE C 72 " pdb=" OH TYR C 177 " model vdw 2.304 2.440 nonbonded pdb=" O ILE B 72 " pdb=" OH TYR B 177 " model vdw 2.304 2.440 nonbonded pdb=" O ILE E 72 " pdb=" OH TYR E 177 " model vdw 2.305 2.440 nonbonded pdb=" O ILE A 72 " pdb=" OH TYR A 177 " model vdw 2.305 2.440 nonbonded pdb=" O ILE F 72 " pdb=" OH TYR F 177 " model vdw 2.305 2.440 ... (remaining 69297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.980 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.060 Find NCS groups from input model: 0.470 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.006 0.069 9828 Z= 0.352 Angle : 0.716 8.849 13308 Z= 0.421 Chirality : 0.043 0.141 1524 Planarity : 0.005 0.028 1608 Dihedral : 14.155 71.487 3498 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.27 % Allowed : 7.39 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.21), residues: 1152 helix: -1.10 (0.15), residues: 828 sheet: -0.68 (0.55), residues: 102 loop : -2.78 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 25 HIS 0.001 0.000 HIS F 95 PHE 0.011 0.001 PHE C 52 TYR 0.016 0.002 TYR C 17 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9025 (mm-30) REVERT: B 100 MET cc_start: 0.8049 (tmm) cc_final: 0.7741 (tmm) REVERT: B 166 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9033 (mm-30) REVERT: B 231 VAL cc_start: 0.8127 (p) cc_final: 0.7762 (p) REVERT: C 166 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8978 (mm-30) REVERT: C 213 MET cc_start: 0.9159 (mmm) cc_final: 0.8923 (mmm) REVERT: F 166 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9030 (mm-30) outliers start: 24 outliers final: 7 residues processed: 204 average time/residue: 0.2289 time to fit residues: 63.3489 Evaluate side-chains 104 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain F residue 98 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 50.0000 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9828 Z= 0.218 Angle : 0.580 5.837 13308 Z= 0.304 Chirality : 0.039 0.190 1524 Planarity : 0.003 0.023 1608 Dihedral : 5.227 41.532 1280 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.94 % Allowed : 15.06 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.75 (0.25), residues: 1152 helix: 1.33 (0.18), residues: 828 sheet: 2.96 (0.60), residues: 60 loop : -2.90 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 25 HIS 0.001 0.000 HIS C 194 PHE 0.007 0.001 PHE F 209 TYR 0.011 0.001 TYR A 177 ARG 0.001 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.4014 (mtt-85) cc_final: 0.2927 (tpt170) REVERT: C 47 ASP cc_start: 0.8233 (p0) cc_final: 0.7995 (p0) REVERT: C 166 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8668 (tp30) REVERT: C 213 MET cc_start: 0.9146 (mmm) cc_final: 0.8860 (mmm) REVERT: D 166 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8693 (tp30) REVERT: E 47 ASP cc_start: 0.8410 (p0) cc_final: 0.8192 (p0) REVERT: E 148 ARG cc_start: 0.4218 (mtt-85) cc_final: 0.3059 (tpt170) REVERT: E 227 GLU cc_start: 0.8724 (tp30) cc_final: 0.8327 (tm-30) REVERT: F 47 ASP cc_start: 0.8264 (p0) cc_final: 0.8049 (p0) REVERT: F 148 ARG cc_start: 0.4532 (mtt-85) cc_final: 0.3350 (tpt170) REVERT: F 227 GLU cc_start: 0.8595 (tp30) cc_final: 0.8308 (tm-30) outliers start: 31 outliers final: 22 residues processed: 165 average time/residue: 0.1811 time to fit residues: 43.1474 Evaluate side-chains 144 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN E 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9828 Z= 0.240 Angle : 0.579 8.562 13308 Z= 0.304 Chirality : 0.038 0.202 1524 Planarity : 0.004 0.026 1608 Dihedral : 5.256 41.103 1280 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.55 % Allowed : 15.44 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.76 (0.26), residues: 1152 helix: 2.12 (0.19), residues: 828 sheet: 1.87 (0.59), residues: 72 loop : -2.52 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 25 HIS 0.001 0.000 HIS F 194 PHE 0.020 0.001 PHE B 229 TYR 0.008 0.001 TYR A 177 ARG 0.006 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 149 time to evaluate : 1.203 Fit side-chains REVERT: A 148 ARG cc_start: 0.4073 (mtt-85) cc_final: 0.2936 (tpt170) REVERT: B 148 ARG cc_start: 0.4451 (mtt-85) cc_final: 0.3132 (tpt170) REVERT: C 148 ARG cc_start: 0.4594 (mtt-85) cc_final: 0.3434 (tpt170) REVERT: C 213 MET cc_start: 0.9148 (mmm) cc_final: 0.8928 (mmm) REVERT: D 166 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8697 (tp30) REVERT: E 148 ARG cc_start: 0.4242 (mtt-85) cc_final: 0.3092 (tpt170) REVERT: F 148 ARG cc_start: 0.4472 (mtt-85) cc_final: 0.3368 (tpt170) outliers start: 48 outliers final: 35 residues processed: 185 average time/residue: 0.1933 time to fit residues: 51.1799 Evaluate side-chains 167 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.0060 chunk 29 optimal weight: 8.9990 overall best weight: 1.6602 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9828 Z= 0.207 Angle : 0.570 7.568 13308 Z= 0.300 Chirality : 0.037 0.161 1524 Planarity : 0.003 0.024 1608 Dihedral : 5.099 40.470 1280 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.94 % Allowed : 17.42 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.11 (0.26), residues: 1152 helix: 2.31 (0.19), residues: 834 sheet: 1.79 (0.60), residues: 72 loop : -2.15 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 25 HIS 0.001 0.000 HIS B 74 PHE 0.020 0.001 PHE A 229 TYR 0.007 0.001 TYR D 177 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 1.144 Fit side-chains REVERT: A 148 ARG cc_start: 0.4201 (mtt-85) cc_final: 0.3018 (tpt170) REVERT: B 31 ILE cc_start: 0.9409 (tp) cc_final: 0.9169 (tt) REVERT: B 148 ARG cc_start: 0.4544 (mtt-85) cc_final: 0.3196 (tpt170) REVERT: C 148 ARG cc_start: 0.4464 (mtt-85) cc_final: 0.3349 (tpt170) REVERT: C 213 MET cc_start: 0.9153 (mmm) cc_final: 0.8939 (mmm) REVERT: D 148 ARG cc_start: 0.3812 (mtt-85) cc_final: 0.2924 (tpt170) REVERT: E 148 ARG cc_start: 0.4380 (mtt-85) cc_final: 0.3167 (tpt170) REVERT: F 148 ARG cc_start: 0.4454 (mtt-85) cc_final: 0.3389 (tpt170) outliers start: 31 outliers final: 28 residues processed: 177 average time/residue: 0.1905 time to fit residues: 48.8309 Evaluate side-chains 168 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 27 optimal weight: 0.0470 overall best weight: 1.4882 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9828 Z= 0.181 Angle : 0.552 6.149 13308 Z= 0.291 Chirality : 0.036 0.124 1524 Planarity : 0.003 0.025 1608 Dihedral : 4.888 39.975 1278 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.56 % Allowed : 20.36 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.31 (0.26), residues: 1152 helix: 2.46 (0.19), residues: 834 sheet: 1.71 (0.60), residues: 72 loop : -2.00 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 25 HIS 0.001 0.000 HIS E 74 PHE 0.016 0.001 PHE A 229 TYR 0.006 0.001 TYR C 177 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.145 Fit side-chains REVERT: A 84 PHE cc_start: 0.8785 (m-80) cc_final: 0.8554 (m-10) REVERT: A 148 ARG cc_start: 0.4151 (mtt-85) cc_final: 0.2959 (tpt170) REVERT: B 31 ILE cc_start: 0.9415 (tp) cc_final: 0.9127 (tt) REVERT: B 148 ARG cc_start: 0.4501 (mtt-85) cc_final: 0.3201 (tpt170) REVERT: C 148 ARG cc_start: 0.4397 (mtt-85) cc_final: 0.3352 (tpt170) REVERT: C 213 MET cc_start: 0.9162 (mmm) cc_final: 0.8952 (mmm) REVERT: D 148 ARG cc_start: 0.3919 (mtt-85) cc_final: 0.2988 (tpt170) REVERT: D 197 ASP cc_start: 0.8297 (m-30) cc_final: 0.7642 (p0) REVERT: E 148 ARG cc_start: 0.4402 (mtt-85) cc_final: 0.3181 (tpt170) REVERT: F 148 ARG cc_start: 0.4446 (mtt-85) cc_final: 0.3396 (tpt170) outliers start: 27 outliers final: 25 residues processed: 170 average time/residue: 0.1891 time to fit residues: 46.1083 Evaluate side-chains 165 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9828 Z= 0.274 Angle : 0.603 6.238 13308 Z= 0.317 Chirality : 0.038 0.127 1524 Planarity : 0.003 0.026 1608 Dihedral : 5.059 41.413 1278 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.79 % Allowed : 19.79 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.33 (0.26), residues: 1152 helix: 2.44 (0.19), residues: 834 sheet: 2.51 (0.63), residues: 60 loop : -1.91 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 25 HIS 0.001 0.000 HIS D 74 PHE 0.014 0.001 PHE A 229 TYR 0.005 0.001 TYR D 177 ARG 0.003 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 1.245 Fit side-chains REVERT: A 84 PHE cc_start: 0.8858 (m-80) cc_final: 0.8648 (m-10) REVERT: A 148 ARG cc_start: 0.4082 (mtt-85) cc_final: 0.2972 (tpt170) REVERT: B 31 ILE cc_start: 0.9356 (tp) cc_final: 0.9113 (tt) REVERT: B 148 ARG cc_start: 0.4498 (mtt-85) cc_final: 0.3184 (tpt170) REVERT: C 148 ARG cc_start: 0.4369 (mtt-85) cc_final: 0.3268 (tpt170) REVERT: C 213 MET cc_start: 0.9162 (mmm) cc_final: 0.8960 (mmm) REVERT: D 84 PHE cc_start: 0.8861 (m-80) cc_final: 0.8612 (m-10) REVERT: D 148 ARG cc_start: 0.3761 (mtt-85) cc_final: 0.2838 (tpt170) REVERT: E 148 ARG cc_start: 0.4474 (mtt-85) cc_final: 0.3146 (tpt170) REVERT: F 148 ARG cc_start: 0.4377 (mtt-85) cc_final: 0.3334 (tpt170) outliers start: 40 outliers final: 31 residues processed: 166 average time/residue: 0.1988 time to fit residues: 47.7028 Evaluate side-chains 161 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.0000 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9828 Z= 0.161 Angle : 0.565 8.593 13308 Z= 0.292 Chirality : 0.036 0.126 1524 Planarity : 0.003 0.027 1608 Dihedral : 4.816 38.827 1278 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.80 % Allowed : 20.83 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.55 (0.26), residues: 1152 helix: 2.58 (0.19), residues: 834 sheet: 2.47 (0.63), residues: 60 loop : -1.75 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 25 HIS 0.001 0.001 HIS F 74 PHE 0.012 0.001 PHE A 229 TYR 0.006 0.001 TYR D 177 ARG 0.003 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.133 Fit side-chains REVERT: A 84 PHE cc_start: 0.8844 (m-80) cc_final: 0.8633 (m-10) REVERT: A 148 ARG cc_start: 0.3916 (mtt-85) cc_final: 0.3032 (tpt170) REVERT: A 197 ASP cc_start: 0.8270 (m-30) cc_final: 0.7578 (p0) REVERT: A 227 GLU cc_start: 0.8783 (tp30) cc_final: 0.8563 (tp30) REVERT: B 31 ILE cc_start: 0.9339 (tp) cc_final: 0.9093 (tt) REVERT: B 148 ARG cc_start: 0.4342 (mtt-85) cc_final: 0.3298 (tpt170) REVERT: C 148 ARG cc_start: 0.4346 (mtt-85) cc_final: 0.3407 (tpt170) REVERT: C 166 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8863 (mm-30) REVERT: C 213 MET cc_start: 0.9159 (mmm) cc_final: 0.8954 (mmm) REVERT: D 84 PHE cc_start: 0.8849 (m-80) cc_final: 0.8589 (m-10) REVERT: D 148 ARG cc_start: 0.3754 (mtt-85) cc_final: 0.2973 (tpt170) REVERT: D 197 ASP cc_start: 0.8223 (m-30) cc_final: 0.7540 (p0) REVERT: E 148 ARG cc_start: 0.4467 (mtt-85) cc_final: 0.3174 (tpt170) REVERT: F 148 ARG cc_start: 0.4456 (mtt-85) cc_final: 0.3501 (tpt170) outliers start: 19 outliers final: 16 residues processed: 150 average time/residue: 0.2011 time to fit residues: 43.3294 Evaluate side-chains 144 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 50.0000 chunk 86 optimal weight: 50.0000 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 50.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9828 Z= 0.232 Angle : 0.599 8.581 13308 Z= 0.310 Chirality : 0.037 0.128 1524 Planarity : 0.003 0.027 1608 Dihedral : 4.071 18.361 1266 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.65 % Allowed : 20.27 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.60 (0.26), residues: 1152 helix: 2.59 (0.19), residues: 834 sheet: 2.41 (0.63), residues: 60 loop : -1.56 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 25 HIS 0.001 0.000 HIS F 74 PHE 0.011 0.001 PHE A 229 TYR 0.005 0.001 TYR C 92 ARG 0.003 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.129 Fit side-chains REVERT: A 84 PHE cc_start: 0.8878 (m-80) cc_final: 0.8678 (m-10) REVERT: A 148 ARG cc_start: 0.3750 (mtt-85) cc_final: 0.2977 (tpt170) REVERT: A 227 GLU cc_start: 0.8823 (tp30) cc_final: 0.8610 (tp30) REVERT: B 31 ILE cc_start: 0.9354 (tp) cc_final: 0.9123 (tt) REVERT: B 148 ARG cc_start: 0.4194 (mtt-85) cc_final: 0.3180 (tpt170) REVERT: C 148 ARG cc_start: 0.4324 (mtt-85) cc_final: 0.3321 (tpt170) REVERT: C 227 GLU cc_start: 0.8900 (tp30) cc_final: 0.8686 (tp30) REVERT: D 84 PHE cc_start: 0.8897 (m-80) cc_final: 0.8646 (m-10) REVERT: D 100 MET cc_start: 0.8050 (tmm) cc_final: 0.7655 (tmm) REVERT: D 148 ARG cc_start: 0.3768 (mtt-85) cc_final: 0.2935 (tpt170) REVERT: D 166 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8877 (mm-30) REVERT: E 148 ARG cc_start: 0.4460 (mtt-85) cc_final: 0.3191 (tpt170) REVERT: E 166 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8865 (mm-30) REVERT: F 148 ARG cc_start: 0.4395 (mtt-85) cc_final: 0.3442 (tpt170) outliers start: 28 outliers final: 28 residues processed: 147 average time/residue: 0.1875 time to fit residues: 39.8310 Evaluate side-chains 153 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 105 optimal weight: 50.0000 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 50.0000 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8319 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9828 Z= 0.158 Angle : 0.563 8.328 13308 Z= 0.292 Chirality : 0.035 0.121 1524 Planarity : 0.003 0.028 1608 Dihedral : 3.860 16.723 1266 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.52 % Allowed : 21.88 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.60 (0.26), residues: 1152 helix: 2.61 (0.18), residues: 834 sheet: 2.27 (0.63), residues: 60 loop : -1.58 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 25 HIS 0.001 0.000 HIS A 194 PHE 0.011 0.001 PHE A 229 TYR 0.005 0.001 TYR C 177 ARG 0.003 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.157 Fit side-chains REVERT: A 84 PHE cc_start: 0.8846 (m-80) cc_final: 0.8621 (m-10) REVERT: A 148 ARG cc_start: 0.3960 (mtt-85) cc_final: 0.3134 (tpt170) REVERT: A 197 ASP cc_start: 0.8251 (m-30) cc_final: 0.7465 (p0) REVERT: A 227 GLU cc_start: 0.8812 (tp30) cc_final: 0.8596 (tp30) REVERT: B 31 ILE cc_start: 0.9332 (tp) cc_final: 0.9105 (tt) REVERT: B 148 ARG cc_start: 0.4353 (mtt-85) cc_final: 0.3245 (tpt170) REVERT: C 148 ARG cc_start: 0.4488 (mtt-85) cc_final: 0.3403 (tpt170) REVERT: D 84 PHE cc_start: 0.8858 (m-80) cc_final: 0.8600 (m-10) REVERT: D 148 ARG cc_start: 0.3854 (mtt-85) cc_final: 0.3033 (tpt170) REVERT: E 148 ARG cc_start: 0.4392 (mtt-85) cc_final: 0.3239 (tpt170) REVERT: F 148 ARG cc_start: 0.4357 (mtt-85) cc_final: 0.3506 (tpt170) outliers start: 16 outliers final: 14 residues processed: 136 average time/residue: 0.1905 time to fit residues: 37.7539 Evaluate side-chains 131 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.0370 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3860 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9828 Z= 0.180 Angle : 0.579 7.827 13308 Z= 0.298 Chirality : 0.036 0.121 1524 Planarity : 0.003 0.027 1608 Dihedral : 3.840 15.137 1266 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.52 % Allowed : 21.97 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.67 (0.26), residues: 1152 helix: 2.65 (0.19), residues: 834 sheet: 2.18 (0.64), residues: 60 loop : -1.50 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 25 HIS 0.001 0.000 HIS C 74 PHE 0.011 0.001 PHE A 229 TYR 0.005 0.001 TYR D 177 ARG 0.003 0.000 ARG E 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.064 Fit side-chains REVERT: A 84 PHE cc_start: 0.8888 (m-80) cc_final: 0.8648 (m-10) REVERT: A 148 ARG cc_start: 0.3760 (mtt-85) cc_final: 0.3101 (tpt170) REVERT: B 31 ILE cc_start: 0.9343 (tp) cc_final: 0.9136 (tt) REVERT: B 148 ARG cc_start: 0.4252 (mtt-85) cc_final: 0.3223 (tpt170) REVERT: C 148 ARG cc_start: 0.4384 (mtt-85) cc_final: 0.3465 (tpt170) REVERT: D 84 PHE cc_start: 0.8900 (m-80) cc_final: 0.8645 (m-10) REVERT: D 148 ARG cc_start: 0.3829 (mtt-85) cc_final: 0.3044 (tpt170) REVERT: E 148 ARG cc_start: 0.4335 (mtt-85) cc_final: 0.3211 (tpt170) REVERT: F 84 PHE cc_start: 0.8891 (m-80) cc_final: 0.8667 (m-10) REVERT: F 148 ARG cc_start: 0.4330 (mtt-85) cc_final: 0.3480 (tpt170) REVERT: F 166 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8853 (mm-30) outliers start: 16 outliers final: 16 residues processed: 131 average time/residue: 0.1995 time to fit residues: 37.5340 Evaluate side-chains 128 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.101718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073028 restraints weight = 24833.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075601 restraints weight = 10865.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077061 restraints weight = 7019.898| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9828 Z= 0.160 Angle : 0.564 7.349 13308 Z= 0.291 Chirality : 0.035 0.118 1524 Planarity : 0.003 0.029 1608 Dihedral : 3.764 15.465 1266 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.61 % Allowed : 21.69 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.67 (0.26), residues: 1152 helix: 2.66 (0.18), residues: 834 sheet: 2.06 (0.65), residues: 60 loop : -1.52 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 25 HIS 0.000 0.000 HIS C 74 PHE 0.011 0.001 PHE A 229 TYR 0.006 0.001 TYR D 177 ARG 0.004 0.000 ARG A 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1729.72 seconds wall clock time: 31 minutes 59.48 seconds (1919.48 seconds total)