Starting phenix.real_space_refine (version: dev) on Sat Feb 25 18:58:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/02_2023/6pwx_20514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/02_2023/6pwx_20514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/02_2023/6pwx_20514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/02_2023/6pwx_20514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/02_2023/6pwx_20514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwx_20514/02_2023/6pwx_20514.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11964 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G ASP 123": "OD1" <-> "OD2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ASP 81": "OD1" <-> "OD2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "M GLU 91": "OE1" <-> "OE2" Residue "N TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14411 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2447 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.32, per 1000 atoms: 0.58 Number of scatterers: 14411 At special positions: 0 Unit cell: (102.01, 129.28, 123.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 292 15.00 O 3267 8.00 N 2673 7.00 C 8152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.42 Conformation dependent library (CDL) restraints added in 1.5 seconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 51.7% alpha, 12.1% beta 147 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 6.52 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'H' and resid 24 through 29 removed outlier: 4.311A pdb=" N GLN H 27 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.951A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.534A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 45 through 73 removed outlier: 4.339A pdb=" N VAL I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 removed outlier: 3.562A pdb=" N ASN I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 Processing helix chain 'J' and resid 52 through 81 Processing helix chain 'J' and resid 87 through 99 Processing helix chain 'J' and resid 100 through 120 removed outlier: 3.685A pdb=" N ALA J 104 " --> pdb=" O PRO J 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.484A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 101 through 121 removed outlier: 3.863A pdb=" N ALA N 121 " --> pdb=" O LYS N 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.310A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.951A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.533A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.394A pdb=" N VAL A 318 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 309 " --> pdb=" O TRP A 303 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP A 303 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 311 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 301 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 313 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.652A pdb=" N ILE A 48 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 50 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 7.102A pdb=" N ALA A 84 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 72 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 82 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP A 74 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 80 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP A 94 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 100 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 115 removed outlier: 4.062A pdb=" N LYS A 112 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 159 removed outlier: 6.976A pdb=" N LYS A 179 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 185 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 259 removed outlier: 6.142A pdb=" N GLU A 280 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 286 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.050A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.169A pdb=" N ARG I 42 " --> pdb=" O ILE J 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.382A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.055A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 77 through 78 479 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 8.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3042 1.33 - 1.45: 4521 1.45 - 1.57: 7085 1.57 - 1.69: 582 1.69 - 1.81: 41 Bond restraints: 15271 Sorted by residual: bond pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" C3' DC P 126 " pdb=" O3' DC P 126 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CG GLU H 52 " pdb=" CD GLU H 52 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG ASP K 106 " pdb=" OD1 ASP K 106 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.41e+00 ... (remaining 15266 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.74: 1565 105.74 - 112.80: 8523 112.80 - 119.86: 4972 119.86 - 126.93: 6067 126.93 - 133.99: 788 Bond angle restraints: 21915 Sorted by residual: angle pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " pdb=" CD GLU H 52 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.70e+00 3.46e-01 1.34e+01 angle pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " pdb=" CD GLU L 52 " ideal model delta sigma weight residual 112.60 118.76 -6.16 1.70e+00 3.46e-01 1.32e+01 angle pdb=" N ASP G 106 " pdb=" CA ASP G 106 " pdb=" CB ASP G 106 " ideal model delta sigma weight residual 110.28 115.41 -5.13 1.55e+00 4.16e-01 1.10e+01 ... (remaining 21910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.55: 6255 26.55 - 53.09: 1487 53.09 - 79.64: 394 79.64 - 106.18: 13 106.18 - 132.73: 3 Dihedral angle restraints: 8152 sinusoidal: 5039 harmonic: 3113 Sorted by residual: dihedral pdb=" CA ILE L 50 " pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE H 50 " pdb=" C ILE H 50 " pdb=" N TYR H 51 " pdb=" CA TYR H 51 " ideal model delta harmonic sigma weight residual 180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C4' DG P 94 " pdb=" C3' DG P 94 " pdb=" O3' DG P 94 " pdb=" P DG P 95 " ideal model delta sinusoidal sigma weight residual -140.00 -7.27 -132.73 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 8149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1634 0.028 - 0.057: 609 0.057 - 0.085: 165 0.085 - 0.113: 84 0.113 - 0.141: 17 Chirality restraints: 2509 Sorted by residual: chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL A 125 " pdb=" N VAL A 125 " pdb=" C VAL A 125 " pdb=" CB VAL A 125 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2506 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 64 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C ASN L 64 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN L 64 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL L 65 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 64 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASN H 64 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN H 64 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL H 65 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC O 80 " -0.007 2.00e-02 2.50e+03 1.33e-02 4.00e+00 pdb=" N1 DC O 80 " 0.013 2.00e-02 2.50e+03 pdb=" C2 DC O 80 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DC O 80 " -0.018 2.00e-02 2.50e+03 pdb=" N3 DC O 80 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC O 80 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC O 80 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC O 80 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC O 80 " -0.006 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 419 2.66 - 3.22: 13370 3.22 - 3.78: 29040 3.78 - 4.34: 34913 4.34 - 4.90: 49905 Nonbonded interactions: 127647 Sorted by model distance: nonbonded pdb=" N2 DG O 83 " pdb=" O2 DC P 65 " model vdw 2.098 2.496 nonbonded pdb=" OG1 THR A 217 " pdb=" OD1 ASP A 219 " model vdw 2.178 2.440 nonbonded pdb=" OE1 GLU L 52 " pdb=" N GLU L 53 " model vdw 2.219 2.520 nonbonded pdb=" OE1 GLU H 52 " pdb=" N GLU H 53 " model vdw 2.220 2.520 nonbonded pdb=" OP1 DA P 102 " pdb=" N LYS L 79 " model vdw 2.236 2.520 ... (remaining 127642 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 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'M' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 27 5.16 5 C 8152 2.51 5 N 2673 2.21 5 O 3267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 9.730 Check model and map are aligned: 0.240 Process input model: 47.810 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.003 0.048 15271 Z= 0.174 Angle : 0.591 8.229 21915 Z= 0.368 Chirality : 0.036 0.141 2509 Planarity : 0.003 0.038 1765 Dihedral : 27.240 132.729 6140 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.24), residues: 1056 helix: -0.03 (0.20), residues: 546 sheet: -2.08 (0.44), residues: 134 loop : -2.45 (0.28), residues: 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 427 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 11 residues processed: 436 average time/residue: 0.3349 time to fit residues: 197.4768 Evaluate side-chains 332 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 321 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1334 time to fit residues: 4.0571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 197 ASN A 274 HIS G 39 HIS G 68 GLN H 25 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 ASN I 68 ASN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 68 GLN K 76 GLN K 108 ASN M 24 GLN M 104 GLN N 46 HIS N 92 GLN L 25 ASN L 64 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 15271 Z= 0.241 Angle : 0.618 8.218 21915 Z= 0.357 Chirality : 0.038 0.181 2509 Planarity : 0.005 0.066 1765 Dihedral : 30.656 132.570 4116 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1056 helix: 1.21 (0.22), residues: 526 sheet: -1.71 (0.43), residues: 144 loop : -1.83 (0.29), residues: 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 359 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 359 average time/residue: 0.2691 time to fit residues: 139.5688 Evaluate side-chains 294 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN G 108 ASN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 ASN I 68 ASN K 39 HIS ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 15271 Z= 0.333 Angle : 0.655 9.032 21915 Z= 0.378 Chirality : 0.039 0.147 2509 Planarity : 0.005 0.051 1765 Dihedral : 30.664 131.359 4116 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1056 helix: 1.28 (0.21), residues: 542 sheet: -1.57 (0.44), residues: 144 loop : -1.62 (0.30), residues: 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 336 average time/residue: 0.2908 time to fit residues: 138.4193 Evaluate side-chains 287 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 76 GLN G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 15271 Z= 0.254 Angle : 0.632 7.517 21915 Z= 0.367 Chirality : 0.038 0.200 2509 Planarity : 0.004 0.053 1765 Dihedral : 30.627 131.429 4116 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1056 helix: 1.49 (0.22), residues: 544 sheet: -1.48 (0.44), residues: 144 loop : -1.47 (0.31), residues: 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.2735 time to fit residues: 136.1649 Evaluate side-chains 277 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 15271 Z= 0.377 Angle : 0.683 8.683 21915 Z= 0.396 Chirality : 0.040 0.173 2509 Planarity : 0.005 0.055 1765 Dihedral : 30.648 134.074 4116 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1056 helix: 1.33 (0.22), residues: 536 sheet: -1.42 (0.45), residues: 144 loop : -1.53 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2735 time to fit residues: 127.0600 Evaluate side-chains 263 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS A 291 HIS G 68 GLN G 76 GLN G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15271 Z= 0.220 Angle : 0.628 7.830 21915 Z= 0.363 Chirality : 0.038 0.181 2509 Planarity : 0.005 0.079 1765 Dihedral : 30.586 131.872 4116 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1056 helix: 1.53 (0.22), residues: 542 sheet: -1.23 (0.46), residues: 144 loop : -1.39 (0.31), residues: 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2753 time to fit residues: 131.5318 Evaluate side-chains 277 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.0040 chunk 58 optimal weight: 4.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 15271 Z= 0.221 Angle : 0.628 8.965 21915 Z= 0.364 Chirality : 0.038 0.167 2509 Planarity : 0.005 0.080 1765 Dihedral : 30.494 132.039 4116 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1056 helix: 1.46 (0.22), residues: 536 sheet: -1.16 (0.46), residues: 149 loop : -1.37 (0.31), residues: 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2740 time to fit residues: 133.9058 Evaluate side-chains 282 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 76 GLN G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 15271 Z= 0.290 Angle : 0.659 8.902 21915 Z= 0.379 Chirality : 0.039 0.169 2509 Planarity : 0.005 0.073 1765 Dihedral : 30.484 132.043 4116 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1056 helix: 1.35 (0.22), residues: 534 sheet: -1.31 (0.46), residues: 146 loop : -1.19 (0.31), residues: 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2706 time to fit residues: 123.4648 Evaluate side-chains 269 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 124 optimal weight: 0.4980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 15271 Z= 0.206 Angle : 0.627 8.628 21915 Z= 0.360 Chirality : 0.037 0.156 2509 Planarity : 0.005 0.062 1765 Dihedral : 30.402 132.901 4116 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1056 helix: 1.38 (0.22), residues: 538 sheet: -1.16 (0.46), residues: 151 loop : -1.08 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.2669 time to fit residues: 130.4211 Evaluate side-chains 280 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN G 76 GLN G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 15271 Z= 0.234 Angle : 0.646 9.023 21915 Z= 0.368 Chirality : 0.038 0.182 2509 Planarity : 0.004 0.062 1765 Dihedral : 30.374 132.913 4116 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1056 helix: 1.37 (0.22), residues: 536 sheet: -1.15 (0.45), residues: 151 loop : -1.07 (0.32), residues: 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2674 time to fit residues: 125.8530 Evaluate side-chains 276 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS G 68 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.044495 restraints weight = 78160.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046006 restraints weight = 37402.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046956 restraints weight = 23339.338| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 15271 Z= 0.228 Angle : 0.643 8.729 21915 Z= 0.368 Chirality : 0.038 0.181 2509 Planarity : 0.005 0.067 1765 Dihedral : 30.342 132.977 4116 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1056 helix: 1.27 (0.22), residues: 536 sheet: -1.09 (0.45), residues: 151 loop : -0.94 (0.32), residues: 369 =============================================================================== Job complete usr+sys time: 3003.40 seconds wall clock time: 55 minutes 39.97 seconds (3339.97 seconds total)