Starting phenix.real_space_refine on Sat Dec 9 00:50:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/12_2023/7xqi_33397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/12_2023/7xqi_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_33397/12_2023/7xqi_33397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/12_2023/7xqi_33397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/12_2023/7xqi_33397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqi_33397/12_2023/7xqi_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.36, per 1000 atoms: 0.56 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: 3.80 Conformation dependent library (CDL) restraints added in 2.0 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: 0.93 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: 3.41 Time building geometry restraints manager: 4.04 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: 3.630 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: 3.990 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.250 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- 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 : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 204 average time/residue: 0.2409 time to fit residues: 66.7465 Evaluate side-chains 102 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1196 time to fit residues: 3.0366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 29 optimal weight: 50.0000 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 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: 0.8358 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9828 Z= 0.212 Angle : 0.581 5.613 13308 Z= 0.304 Chirality : 0.039 0.187 1524 Planarity : 0.003 0.024 1608 Dihedral : 4.229 21.713 1266 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.37 % Allowed : 14.49 % Favored : 83.14 % 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: 2.93 (0.59), 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: 25 poor density : 147 time to evaluate : 1.287 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 166 average time/residue: 0.1959 time to fit residues: 46.9005 Evaluate side-chains 126 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0956 time to fit residues: 4.2349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 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: 2.7988 ------------------------------------------------------------------------------- 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: 0.8389 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9828 Z= 0.286 Angle : 0.614 8.715 13308 Z= 0.322 Chirality : 0.039 0.210 1524 Planarity : 0.004 0.026 1608 Dihedral : 4.400 28.213 1266 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.31 % Allowed : 16.86 % Favored : 79.83 % 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: 1.67 (0.27), residues: 1152 helix: 2.04 (0.19), residues: 828 sheet: 1.86 (0.59), residues: 72 loop : -2.49 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 25 HIS 0.001 0.000 HIS F 194 PHE 0.020 0.001 PHE B 229 TYR 0.008 0.001 TYR C 177 ARG 0.003 0.000 ARG C 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 174 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.229 Fit side-chains outliers start: 35 outliers final: 22 residues processed: 164 average time/residue: 0.1728 time to fit residues: 42.3115 Evaluate side-chains 140 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0967 time to fit residues: 5.3057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 50.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN C 55 ASN E 55 ASN F 15 GLN F 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9828 Z= 0.280 Angle : 0.612 9.175 13308 Z= 0.320 Chirality : 0.039 0.202 1524 Planarity : 0.003 0.024 1608 Dihedral : 4.450 31.246 1266 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.85 % Allowed : 19.22 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.97 (0.26), residues: 1152 helix: 2.20 (0.19), residues: 840 sheet: 2.75 (0.62), residues: 60 loop : -2.38 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 25 HIS 0.001 0.000 HIS F 74 PHE 0.020 0.001 PHE A 229 TYR 0.007 0.001 TYR D 177 ARG 0.003 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 162 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.271 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 158 average time/residue: 0.1779 time to fit residues: 42.0117 Evaluate side-chains 136 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0851 time to fit residues: 2.2941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 1 optimal weight: 0.0170 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 0.0020 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.2028 ------------------------------------------------------------------------------- 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: 0.8337 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9828 Z= 0.173 Angle : 0.559 7.390 13308 Z= 0.292 Chirality : 0.036 0.152 1524 Planarity : 0.003 0.025 1608 Dihedral : 4.096 23.709 1266 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.09 % Allowed : 23.01 % Favored : 76.89 % 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: 2.20 (0.26), residues: 1152 helix: 2.46 (0.19), residues: 828 sheet: 1.67 (0.61), residues: 72 loop : -2.26 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 25 HIS 0.001 0.000 HIS A 194 PHE 0.015 0.001 PHE A 229 TYR 0.006 0.001 TYR F 177 ARG 0.002 0.000 ARG F 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 145 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.188 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 144 average time/residue: 0.1608 time to fit residues: 35.7163 Evaluate side-chains 124 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0881 time to fit residues: 1.8795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8328 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9828 Z= 0.180 Angle : 0.560 6.164 13308 Z= 0.294 Chirality : 0.036 0.129 1524 Planarity : 0.003 0.027 1608 Dihedral : 3.905 16.464 1266 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.57 % Allowed : 22.73 % 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: 2.38 (0.26), residues: 1152 helix: 2.58 (0.19), residues: 828 sheet: 1.51 (0.61), residues: 72 loop : -2.06 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 25 HIS 0.001 0.000 HIS F 194 PHE 0.013 0.001 PHE A 229 TYR 0.006 0.001 TYR A 177 ARG 0.004 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 125 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.205 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 124 average time/residue: 0.1644 time to fit residues: 31.5774 Evaluate side-chains 114 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 109 optimal weight: 0.0170 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.8824 ------------------------------------------------------------------------------- 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: 0.8310 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9828 Z= 0.164 Angle : 0.546 7.129 13308 Z= 0.282 Chirality : 0.036 0.118 1524 Planarity : 0.003 0.028 1608 Dihedral : 3.879 17.061 1266 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.66 % Allowed : 22.92 % 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: 2.44 (0.26), residues: 1152 helix: 2.66 (0.19), residues: 828 sheet: 2.36 (0.66), residues: 60 loop : -2.24 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 25 HIS 0.001 0.000 HIS E 194 PHE 0.012 0.001 PHE A 229 TYR 0.005 0.001 TYR C 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 125 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.181 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 123 average time/residue: 0.1743 time to fit residues: 32.5885 Evaluate side-chains 108 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0829 time to fit residues: 1.6929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 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: 1.3784 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9828 Z= 0.180 Angle : 0.563 9.047 13308 Z= 0.290 Chirality : 0.036 0.121 1524 Planarity : 0.003 0.027 1608 Dihedral : 3.891 17.038 1266 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.57 % Allowed : 23.48 % Favored : 75.95 % 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: 2.53 (0.26), residues: 1152 helix: 2.63 (0.18), residues: 834 sheet: 2.21 (0.67), residues: 60 loop : -1.91 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 25 HIS 0.001 0.000 HIS E 74 PHE 0.023 0.001 PHE D 229 TYR 0.005 0.001 TYR D 177 ARG 0.003 0.000 ARG B 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 116 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.246 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 115 average time/residue: 0.1578 time to fit residues: 28.9483 Evaluate side-chains 113 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1103 time to fit residues: 2.1165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.8955 > 50: distance: 75 - 103: 12.680 distance: 80 - 85: 12.883 distance: 81 - 114: 5.579 distance: 85 - 86: 10.630 distance: 86 - 87: 4.383 distance: 86 - 89: 16.259 distance: 87 - 88: 8.863 distance: 87 - 92: 8.550 distance: 88 - 128: 18.505 distance: 89 - 90: 9.034 distance: 89 - 91: 10.001 distance: 92 - 93: 4.658 distance: 93 - 94: 6.939 distance: 93 - 96: 9.532 distance: 94 - 95: 9.429 distance: 94 - 103: 11.904 distance: 95 - 135: 16.114 distance: 96 - 97: 8.619 distance: 97 - 98: 8.349 distance: 98 - 99: 5.627 distance: 99 - 100: 6.526 distance: 100 - 101: 6.533 distance: 100 - 102: 8.190 distance: 103 - 104: 7.654 distance: 104 - 105: 5.869 distance: 104 - 107: 3.753 distance: 105 - 106: 5.500 distance: 105 - 114: 5.299 distance: 106 - 143: 8.590 distance: 107 - 108: 4.854 distance: 108 - 109: 7.187 distance: 108 - 110: 3.996 distance: 109 - 111: 11.262 distance: 110 - 112: 8.866 distance: 111 - 113: 5.431 distance: 112 - 113: 9.971 distance: 114 - 115: 7.513 distance: 115 - 116: 9.145 distance: 115 - 118: 5.314 distance: 116 - 117: 4.785 distance: 116 - 128: 8.248 distance: 117 - 152: 13.080 distance: 118 - 119: 7.020 distance: 119 - 120: 7.366 distance: 119 - 121: 4.626 distance: 121 - 123: 4.898 distance: 121 - 124: 9.946 distance: 122 - 123: 8.522 distance: 123 - 125: 7.147 distance: 124 - 126: 3.824 distance: 125 - 127: 7.359 distance: 126 - 127: 6.246 distance: 128 - 129: 8.196 distance: 129 - 130: 10.392 distance: 129 - 132: 12.406 distance: 130 - 131: 7.081 distance: 130 - 135: 15.027 distance: 131 - 160: 5.552 distance: 132 - 133: 15.574 distance: 132 - 134: 11.393 distance: 136 - 137: 11.141 distance: 136 - 139: 9.074 distance: 137 - 138: 8.533 distance: 137 - 143: 11.694 distance: 138 - 168: 15.413 distance: 139 - 140: 11.556 distance: 140 - 141: 18.987 distance: 140 - 142: 23.112 distance: 143 - 144: 7.151 distance: 144 - 145: 12.305 distance: 144 - 147: 12.126 distance: 145 - 146: 8.368 distance: 145 - 152: 6.711 distance: 146 - 179: 26.905 distance: 147 - 148: 8.871 distance: 148 - 149: 13.105 distance: 149 - 150: 15.037 distance: 149 - 151: 16.255 distance: 152 - 153: 7.743 distance: 153 - 154: 9.060 distance: 153 - 156: 10.052 distance: 154 - 155: 8.286 distance: 154 - 160: 24.937 distance: 156 - 157: 14.507 distance: 156 - 158: 7.820 distance: 157 - 159: 3.728 distance: 160 - 161: 18.180 distance: 161 - 162: 14.011 distance: 161 - 164: 24.577 distance: 162 - 163: 37.934 distance: 162 - 168: 14.896 distance: 164 - 165: 30.697 distance: 164 - 166: 18.769 distance: 165 - 167: 33.361 distance: 168 - 169: 14.211 distance: 169 - 170: 6.451 distance: 169 - 172: 18.970 distance: 170 - 171: 34.704 distance: 170 - 179: 12.721 distance: 172 - 173: 19.261 distance: 173 - 174: 31.608 distance: 173 - 175: 10.183 distance: 174 - 176: 21.710 distance: 175 - 177: 5.357 distance: 176 - 178: 20.435 distance: 177 - 178: 36.039