Starting phenix.real_space_refine on Wed Feb 14 13:40:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/02_2024/6m4h_30078.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/02_2024/6m4h_30078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/02_2024/6m4h_30078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/02_2024/6m4h_30078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/02_2024/6m4h_30078.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/02_2024/6m4h_30078.pdb" } resolution = 3.9 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= 0.005 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 206 5.49 5 S 16 5.16 5 C 5279 2.51 5 N 1735 2.21 5 O 2184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "H GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9420 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2132 Classifications: {'DNA': 103} Link IDs: {'rna3p': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2090 Classifications: {'DNA': 103} Link IDs: {'rna3p': 102} Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "H" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Time building chain proxies: 5.17, per 1000 atoms: 0.55 Number of scatterers: 9420 At special positions: 0 Unit cell: (97.76, 114.4, 113.36, 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 16 16.00 P 206 15.00 O 2184 8.00 N 1735 7.00 C 5279 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: 5.75 Conformation dependent library (CDL) restraints added in 951.2 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 74.7% alpha, 2.1% beta 98 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.585A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.635A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.647A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 52 through 78 removed outlier: 3.865A pdb=" N GLU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.786A pdb=" N HIS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 93 " --> pdb=" O MET C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.608A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.583A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 30 through 40 Processing helix chain 'G' and resid 50 through 76 removed outlier: 3.865A pdb=" N GLU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.788A pdb=" N HIS G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN G 93 " --> pdb=" O MET G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.702A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.607A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.027A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.336A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.729A pdb=" N THR C 105 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.123A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 316 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 249 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 5.87 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: 1574 1.33 - 1.45: 3361 1.45 - 1.57: 4624 1.57 - 1.69: 412 1.69 - 1.80: 28 Bond restraints: 9999 Sorted by residual: bond pdb=" C ARG G 49 " pdb=" N THR G 50 " ideal model delta sigma weight residual 1.333 1.287 0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N GLU G 79 " pdb=" CA GLU G 79 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.16e-02 7.43e+03 8.37e+00 bond pdb=" N SER G 77 " pdb=" CA SER G 77 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.31e+00 bond pdb=" N SER C 77 " pdb=" CA SER C 77 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 ... (remaining 9994 not shown) Histogram of bond angle deviations from ideal: 97.17 - 104.36: 796 104.36 - 111.54: 5123 111.54 - 118.73: 3076 118.73 - 125.91: 4761 125.91 - 133.10: 639 Bond angle restraints: 14395 Sorted by residual: angle pdb=" N ASN G 76 " pdb=" CA ASN G 76 " pdb=" C ASN G 76 " ideal model delta sigma weight residual 113.37 106.59 6.78 1.38e+00 5.25e-01 2.41e+01 angle pdb=" C ASN G 76 " pdb=" N SER G 77 " pdb=" CA SER G 77 " ideal model delta sigma weight residual 121.87 129.48 -7.61 1.64e+00 3.72e-01 2.15e+01 angle pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " pdb=" CD GLU F 53 " ideal model delta sigma weight residual 112.60 119.77 -7.17 1.70e+00 3.46e-01 1.78e+01 angle pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " pdb=" CD GLU B 53 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 angle pdb=" C CYS E 96 " pdb=" N GLU E 97 " pdb=" CA GLU E 97 " ideal model delta sigma weight residual 120.68 113.87 6.81 1.70e+00 3.46e-01 1.60e+01 ... (remaining 14390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 4392 35.17 - 70.34: 1018 70.34 - 105.51: 46 105.51 - 140.69: 4 140.69 - 175.86: 6 Dihedral angle restraints: 5466 sinusoidal: 3548 harmonic: 1918 Sorted by residual: dihedral pdb=" C4' DC I 34 " pdb=" C3' DC I 34 " pdb=" O3' DC I 34 " pdb=" P DT I 35 " ideal model delta sinusoidal sigma weight residual -140.00 35.86 -175.86 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 32 " pdb=" C3' DT J 32 " pdb=" O3' DT J 32 " pdb=" P DG J 33 " ideal model delta sinusoidal sigma weight residual -140.00 32.37 -172.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA HIS G 92 " pdb=" C HIS G 92 " pdb=" N ASN G 93 " pdb=" CA ASN G 93 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 962 0.035 - 0.071: 491 0.071 - 0.106: 156 0.106 - 0.141: 45 0.141 - 0.176: 12 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA GLU A 97 " pdb=" N GLU A 97 " pdb=" C GLU A 97 " pdb=" CB GLU A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA GLU F 52 " pdb=" N GLU F 52 " pdb=" C GLU F 52 " pdb=" CB GLU F 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA GLU E 97 " pdb=" N GLU E 97 " pdb=" C GLU E 97 " pdb=" CB GLU E 97 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 1663 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 51 " -0.099 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO C 52 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO C 52 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 52 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 67 " 0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C ASN D 67 " -0.071 2.00e-02 2.50e+03 pdb=" O ASN D 67 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP D 68 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 67 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ASN H 67 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN H 67 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP H 68 " -0.024 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 33 2.36 - 3.00: 4572 3.00 - 3.63: 17703 3.63 - 4.27: 25383 4.27 - 4.90: 36252 Nonbonded interactions: 83943 Sorted by model distance: nonbonded pdb=" OP1 DT J 31 " pdb=" OG SER C 20 " model vdw 1.729 2.440 nonbonded pdb=" OP1 DT J 31 " pdb=" CA SER C 20 " model vdw 1.765 3.470 nonbonded pdb=" OP2 DC I 81 " pdb=" N GLY B 48 " model vdw 1.880 2.520 nonbonded pdb=" OP2 DA J 91 " pdb=" NH2 ARG E 69 " model vdw 1.970 2.520 nonbonded pdb=" OP2 DA I 113 " pdb=" NH2 ARG C 39 " model vdw 1.974 2.520 ... (remaining 83938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.250 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 32.470 Find NCS groups from input model: 0.390 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 9999 Z= 0.406 Angle : 0.894 15.598 14395 Z= 0.532 Chirality : 0.048 0.176 1666 Planarity : 0.010 0.153 1100 Dihedral : 29.217 175.856 4222 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 2.85 % Allowed : 2.31 % Favored : 94.84 % 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: -6.02 (0.19), residues: 640 helix: -4.08 (0.11), residues: 444 sheet: None (None), residues: 0 loop : -3.15 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 75 PHE 0.021 0.003 PHE E 67 TYR 0.026 0.003 TYR B 51 ARG 0.006 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 287 time to evaluate : 0.790 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8298 (m) REVERT: B 59 LYS cc_start: 0.8613 (tttt) cc_final: 0.8119 (ttmt) REVERT: B 75 HIS cc_start: 0.7843 (t-90) cc_final: 0.7516 (t-170) REVERT: B 80 THR cc_start: 0.7724 (m) cc_final: 0.7488 (p) REVERT: B 84 MET cc_start: 0.6505 (mmm) cc_final: 0.5995 (mmm) REVERT: C 68 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 62 MET cc_start: 0.8518 (mmm) cc_final: 0.8317 (mmt) REVERT: D 68 ASP cc_start: 0.7408 (t70) cc_final: 0.7073 (t0) REVERT: D 70 PHE cc_start: 0.8359 (t80) cc_final: 0.8127 (t80) REVERT: D 102 LEU cc_start: 0.8193 (mp) cc_final: 0.7980 (mp) REVERT: E 101 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8310 (m) REVERT: F 29 ILE cc_start: 0.8917 (mm) cc_final: 0.8632 (mm) REVERT: F 59 LYS cc_start: 0.8493 (tttt) cc_final: 0.8097 (tttp) REVERT: F 75 HIS cc_start: 0.7852 (t-90) cc_final: 0.7430 (t70) REVERT: G 31 VAL cc_start: 0.7902 (m) cc_final: 0.7430 (p) REVERT: H 37 TYR cc_start: 0.5303 (m-10) cc_final: 0.4674 (m-80) REVERT: H 62 MET cc_start: 0.8383 (mmm) cc_final: 0.8092 (mmt) REVERT: H 68 ASP cc_start: 0.7535 (t70) cc_final: 0.7027 (t0) outliers start: 16 outliers final: 2 residues processed: 292 average time/residue: 0.3480 time to fit residues: 124.6702 Evaluate side-chains 153 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 72 ASN C 108 GLN E 68 GLN G 75 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9999 Z= 0.224 Angle : 0.707 9.814 14395 Z= 0.412 Chirality : 0.040 0.158 1666 Planarity : 0.006 0.055 1100 Dihedral : 33.458 172.474 2966 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.20 % Allowed : 17.44 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.28), residues: 640 helix: -1.40 (0.20), residues: 472 sheet: None (None), residues: 0 loop : -2.37 (0.39), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 109 PHE 0.013 0.002 PHE A 78 TYR 0.018 0.002 TYR F 88 ARG 0.018 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8345 (t) cc_final: 0.8116 (m) REVERT: B 75 HIS cc_start: 0.7778 (t-90) cc_final: 0.7403 (t-170) REVERT: B 80 THR cc_start: 0.7658 (m) cc_final: 0.7393 (p) REVERT: B 97 LEU cc_start: 0.8320 (tp) cc_final: 0.8098 (tp) REVERT: C 31 VAL cc_start: 0.7972 (m) cc_final: 0.7234 (p) REVERT: C 68 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7491 (tm-30) REVERT: C 72 ASN cc_start: 0.7705 (m-40) cc_final: 0.7393 (m-40) REVERT: C 88 ASP cc_start: 0.7063 (t0) cc_final: 0.6714 (t0) REVERT: E 69 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7869 (mtm-85) REVERT: F 59 LYS cc_start: 0.8557 (tttt) cc_final: 0.8319 (tttp) REVERT: F 84 MET cc_start: 0.6802 (tpp) cc_final: 0.6492 (tpt) REVERT: G 31 VAL cc_start: 0.7669 (m) cc_final: 0.7224 (p) REVERT: G 61 TYR cc_start: 0.8232 (t80) cc_final: 0.7787 (t80) outliers start: 18 outliers final: 7 residues processed: 196 average time/residue: 0.2853 time to fit residues: 71.7700 Evaluate side-chains 155 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 108 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 45 GLN G 108 GLN H 84 ASN H 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9999 Z= 0.211 Angle : 0.671 5.929 14395 Z= 0.391 Chirality : 0.039 0.153 1666 Planarity : 0.005 0.046 1100 Dihedral : 33.304 178.502 2963 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.74 % Allowed : 21.17 % Favored : 75.09 % 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: -0.70 (0.31), residues: 640 helix: 0.18 (0.23), residues: 476 sheet: None (None), residues: 0 loop : -2.19 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 75 PHE 0.007 0.001 PHE A 67 TYR 0.018 0.002 TYR C 61 ARG 0.009 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6858 (mt-10) REVERT: B 80 THR cc_start: 0.7724 (m) cc_final: 0.7473 (p) REVERT: C 31 VAL cc_start: 0.7791 (m) cc_final: 0.7261 (p) REVERT: C 88 ASP cc_start: 0.7299 (t0) cc_final: 0.6954 (t0) REVERT: F 63 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6398 (mt-10) REVERT: G 31 VAL cc_start: 0.7894 (m) cc_final: 0.7446 (p) REVERT: G 73 GLU cc_start: 0.7915 (tt0) cc_final: 0.7321 (tm-30) outliers start: 21 outliers final: 16 residues processed: 167 average time/residue: 0.2830 time to fit residues: 61.1130 Evaluate side-chains 152 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain H residue 49 HIS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN G 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9999 Z= 0.227 Angle : 0.667 6.112 14395 Z= 0.386 Chirality : 0.039 0.146 1666 Planarity : 0.004 0.043 1100 Dihedral : 33.220 179.562 2963 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.91 % Allowed : 21.35 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.32), residues: 640 helix: 0.90 (0.23), residues: 476 sheet: None (None), residues: 0 loop : -2.04 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.004 0.001 PHE A 84 TYR 0.028 0.002 TYR B 88 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7877 (mtm-85) REVERT: B 63 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6709 (mt-10) REVERT: B 80 THR cc_start: 0.8137 (m) cc_final: 0.7629 (p) REVERT: C 31 VAL cc_start: 0.8029 (m) cc_final: 0.7481 (p) REVERT: C 68 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7237 (tm-30) REVERT: C 72 ASN cc_start: 0.8073 (m-40) cc_final: 0.7842 (m-40) REVERT: C 88 ASP cc_start: 0.7297 (t0) cc_final: 0.6960 (t0) REVERT: E 69 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8150 (mtm-85) REVERT: E 97 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5710 (mt-10) REVERT: E 133 GLU cc_start: 0.6626 (mp0) cc_final: 0.6176 (mp0) REVERT: F 63 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6646 (mt-10) REVERT: G 31 VAL cc_start: 0.8081 (m) cc_final: 0.7658 (p) outliers start: 22 outliers final: 15 residues processed: 162 average time/residue: 0.3035 time to fit residues: 63.0843 Evaluate side-chains 150 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 49 HIS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 99 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9999 Z= 0.225 Angle : 0.674 10.017 14395 Z= 0.386 Chirality : 0.039 0.152 1666 Planarity : 0.005 0.067 1100 Dihedral : 33.108 179.089 2963 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.56 % Allowed : 24.20 % Favored : 72.24 % 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: 0.71 (0.32), residues: 640 helix: 1.27 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -2.00 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 82 PHE 0.006 0.001 PHE A 78 TYR 0.018 0.002 TYR C 61 ARG 0.011 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.6464 (mp0) cc_final: 0.6007 (mp0) REVERT: B 80 THR cc_start: 0.8302 (m) cc_final: 0.7949 (p) REVERT: C 31 VAL cc_start: 0.8113 (m) cc_final: 0.7547 (p) REVERT: C 88 ASP cc_start: 0.7196 (t0) cc_final: 0.6896 (t0) REVERT: E 69 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8197 (mtm-85) REVERT: G 60 GLU cc_start: 0.8435 (tt0) cc_final: 0.7784 (tt0) outliers start: 20 outliers final: 14 residues processed: 150 average time/residue: 0.2815 time to fit residues: 54.5068 Evaluate side-chains 144 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 49 HIS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 95 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9999 Z= 0.415 Angle : 0.787 7.550 14395 Z= 0.445 Chirality : 0.044 0.200 1666 Planarity : 0.005 0.042 1100 Dihedral : 33.247 175.316 2962 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.98 % Allowed : 23.84 % Favored : 71.17 % 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: 0.58 (0.32), residues: 640 helix: 1.14 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -2.17 (0.42), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.008 0.001 PHE E 78 TYR 0.024 0.003 TYR H 40 ARG 0.014 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8045 (mtm180) REVERT: B 91 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8138 (pttm) REVERT: C 31 VAL cc_start: 0.8797 (m) cc_final: 0.8182 (p) REVERT: C 88 ASP cc_start: 0.7013 (t0) cc_final: 0.6776 (t0) REVERT: E 69 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8275 (mtm-85) REVERT: E 133 GLU cc_start: 0.6931 (mp0) cc_final: 0.6423 (mp0) REVERT: G 31 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8213 (p) outliers start: 28 outliers final: 22 residues processed: 139 average time/residue: 0.2952 time to fit residues: 52.5377 Evaluate side-chains 138 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 49 HIS Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9999 Z= 0.207 Angle : 0.664 7.923 14395 Z= 0.385 Chirality : 0.038 0.138 1666 Planarity : 0.004 0.042 1100 Dihedral : 32.985 177.937 2962 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.56 % Allowed : 24.20 % Favored : 72.24 % 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: 1.04 (0.32), residues: 640 helix: 1.48 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS H 49 PHE 0.012 0.001 PHE E 78 TYR 0.019 0.002 TYR G 61 ARG 0.010 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7930 (mtm-85) REVERT: B 91 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8169 (pttt) REVERT: C 31 VAL cc_start: 0.8450 (m) cc_final: 0.7898 (p) REVERT: C 88 ASP cc_start: 0.6959 (t0) cc_final: 0.6632 (t0) REVERT: D 99 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7537 (mpp80) REVERT: E 69 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8190 (mtm-85) REVERT: G 31 VAL cc_start: 0.8185 (m) cc_final: 0.7720 (p) outliers start: 20 outliers final: 13 residues processed: 150 average time/residue: 0.2736 time to fit residues: 53.0008 Evaluate side-chains 139 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9999 Z= 0.290 Angle : 0.708 7.473 14395 Z= 0.404 Chirality : 0.040 0.167 1666 Planarity : 0.005 0.038 1100 Dihedral : 32.956 178.790 2962 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.09 % Allowed : 25.62 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.32), residues: 640 helix: 1.42 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.019 0.001 PHE H 70 TYR 0.032 0.002 TYR B 88 ARG 0.007 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8118 (mtm180) REVERT: B 91 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8141 (pttm) REVERT: C 31 VAL cc_start: 0.8651 (m) cc_final: 0.8066 (p) REVERT: E 69 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8255 (mtm-85) REVERT: F 88 TYR cc_start: 0.8077 (m-80) cc_final: 0.7183 (m-80) REVERT: G 31 VAL cc_start: 0.8392 (m) cc_final: 0.7897 (p) outliers start: 23 outliers final: 13 residues processed: 136 average time/residue: 0.2828 time to fit residues: 49.8293 Evaluate side-chains 133 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 93 GLN G 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9999 Z= 0.207 Angle : 0.674 8.218 14395 Z= 0.388 Chirality : 0.038 0.145 1666 Planarity : 0.004 0.046 1100 Dihedral : 32.823 178.435 2962 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.20 % Allowed : 26.16 % Favored : 70.64 % 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: 0.99 (0.32), residues: 640 helix: 1.42 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.006 0.001 PHE E 78 TYR 0.035 0.002 TYR F 88 ARG 0.007 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7860 (mtm-85) REVERT: A 133 GLU cc_start: 0.7001 (mp0) cc_final: 0.6687 (mp0) REVERT: B 91 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8115 (pttt) REVERT: C 31 VAL cc_start: 0.8530 (m) cc_final: 0.7956 (p) REVERT: E 69 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8211 (mtm-85) REVERT: G 31 VAL cc_start: 0.8156 (m) cc_final: 0.7700 (p) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.2920 time to fit residues: 54.5292 Evaluate side-chains 130 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 75 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9999 Z= 0.218 Angle : 0.687 7.957 14395 Z= 0.391 Chirality : 0.038 0.155 1666 Planarity : 0.005 0.039 1100 Dihedral : 32.782 176.702 2962 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.49 % Allowed : 27.94 % Favored : 69.57 % 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: 1.03 (0.32), residues: 640 helix: 1.45 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.019 0.001 PHE H 70 TYR 0.038 0.003 TYR H 83 ARG 0.007 0.001 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7041 (mp0) cc_final: 0.6709 (mp0) REVERT: B 91 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8145 (pttt) REVERT: C 31 VAL cc_start: 0.8550 (m) cc_final: 0.7960 (p) REVERT: E 69 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8194 (mtm-85) REVERT: G 31 VAL cc_start: 0.8225 (m) cc_final: 0.7788 (p) outliers start: 14 outliers final: 9 residues processed: 137 average time/residue: 0.3003 time to fit residues: 52.3147 Evaluate side-chains 131 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain H residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.046847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.035919 restraints weight = 65572.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.036961 restraints weight = 33159.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037678 restraints weight = 21719.755| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9999 Z= 0.257 Angle : 0.703 7.107 14395 Z= 0.401 Chirality : 0.039 0.146 1666 Planarity : 0.005 0.091 1100 Dihedral : 32.799 177.908 2962 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.02 % Allowed : 28.11 % Favored : 68.86 % 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: 1.03 (0.32), residues: 640 helix: 1.43 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -1.81 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.004 0.001 PHE E 78 TYR 0.041 0.002 TYR H 83 ARG 0.012 0.001 ARG G 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.35 seconds wall clock time: 35 minutes 26.14 seconds (2126.14 seconds total)