Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 08:52:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/04_2023/6m4h_30078.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/04_2023/6m4h_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_30078/04_2023/6m4h_30078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/04_2023/6m4h_30078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/04_2023/6m4h_30078.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4h_30078/04_2023/6m4h_30078.pdb" } resolution = 3.9 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= 0.005 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-1.21rc1-4938/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: 5.36, per 1000 atoms: 0.57 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: 5.49 Conformation dependent library (CDL) restraints added in 819.5 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: 4.11 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: 2.96 Time building geometry restraints manager: 5.81 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: 4264 35.17 - 70.34: 974 70.34 - 105.51: 46 105.51 - 140.69: 4 140.69 - 175.86: 6 Dihedral angle restraints: 5294 sinusoidal: 3376 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 5291 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.770 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.700 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.050 ------------------------------------------------------------------------------- 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 : 29.176 175.856 4050 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 % 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 *********************** 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 : 0.800 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 outliers start: 16 outliers final: 2 residues processed: 292 average time/residue: 0.3389 time to fit residues: 121.2492 Evaluate side-chains 147 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0887 time to fit residues: 1.3292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 H 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3457 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= 0.225 Angle : 0.713 9.816 14395 Z= 0.414 Chirality : 0.041 0.151 1666 Planarity : 0.006 0.055 1100 Dihedral : 33.885 170.364 2790 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 3.74 % 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: -2.73 (0.28), residues: 640 helix: -1.45 (0.20), residues: 472 sheet: None (None), residues: 0 loop : -2.36 (0.39), residues: 168 *********************** 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 206 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 0.888 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: 21 outliers final: 8 residues processed: 194 average time/residue: 0.3089 time to fit residues: 76.5706 Evaluate side-chains 153 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2199 time to fit residues: 3.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 GLN D 49 HIS G 45 GLN G 108 GLN H 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4100 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= 0.215 Angle : 0.671 5.781 14395 Z= 0.392 Chirality : 0.039 0.147 1666 Planarity : 0.005 0.046 1100 Dihedral : 33.727 176.741 2790 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 3.20 % 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: -0.73 (0.31), residues: 640 helix: 0.13 (0.22), residues: 476 sheet: None (None), residues: 0 loop : -2.11 (0.42), residues: 164 *********************** 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: 18 poor density : 160 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 168 average time/residue: 0.2624 time to fit residues: 57.8122 Evaluate side-chains 146 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0946 time to fit residues: 2.7163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 30.0000 chunk 21 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4682 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= 0.205 Angle : 0.662 6.164 14395 Z= 0.382 Chirality : 0.038 0.140 1666 Planarity : 0.004 0.043 1100 Dihedral : 33.605 178.501 2790 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.32), residues: 640 helix: 0.90 (0.23), residues: 478 sheet: None (None), residues: 0 loop : -1.99 (0.42), residues: 162 *********************** 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 173 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.2833 time to fit residues: 60.9258 Evaluate side-chains 142 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0933 time to fit residues: 2.6425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 71 optimal weight: 0.0000 chunk 20 optimal weight: 0.9980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5010 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 : 0.667 10.124 14395 Z= 0.384 Chirality : 0.038 0.152 1666 Planarity : 0.004 0.050 1100 Dihedral : 33.514 177.650 2790 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 1.07 % 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: 0.82 (0.32), residues: 640 helix: 1.34 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 160 *********************** 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 154 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 153 average time/residue: 0.2601 time to fit residues: 52.3525 Evaluate side-chains 136 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0862 time to fit residues: 1.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 9999 Z= 0.357 Angle : 0.751 8.109 14395 Z= 0.428 Chirality : 0.043 0.184 1666 Planarity : 0.005 0.040 1100 Dihedral : 33.599 178.189 2790 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 2.31 % 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: 0.78 (0.32), residues: 640 helix: 1.28 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -2.05 (0.42), residues: 148 *********************** 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 143 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 137 average time/residue: 0.2886 time to fit residues: 51.0422 Evaluate side-chains 129 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0943 time to fit residues: 2.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9999 Z= 0.202 Angle : 0.675 8.367 14395 Z= 0.388 Chirality : 0.039 0.194 1666 Planarity : 0.004 0.040 1100 Dihedral : 33.362 179.381 2790 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.71 % 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: 1.14 (0.32), residues: 640 helix: 1.55 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -1.88 (0.42), residues: 152 *********************** 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 142 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 140 average time/residue: 0.2419 time to fit residues: 45.5094 Evaluate side-chains 118 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 0.7858 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 9999 Z= 0.287 Angle : 0.708 7.463 14395 Z= 0.404 Chirality : 0.040 0.157 1666 Planarity : 0.004 0.038 1100 Dihedral : 33.378 178.801 2790 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 1.25 % 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: 1.46 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -1.92 (0.41), residues: 150 *********************** 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 127 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 123 average time/residue: 0.2697 time to fit residues: 43.5406 Evaluate side-chains 118 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0855 time to fit residues: 1.4471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5843 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= 0.217 Angle : 0.681 8.183 14395 Z= 0.390 Chirality : 0.039 0.167 1666 Planarity : 0.004 0.037 1100 Dihedral : 33.286 177.648 2790 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.89 % 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: 1.21 (0.33), residues: 640 helix: 1.59 (0.23), residues: 482 sheet: None (None), residues: 0 loop : -1.69 (0.42), residues: 158 *********************** 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 134 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 132 average time/residue: 0.2491 time to fit residues: 44.1407 Evaluate side-chains 121 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1258 time to fit residues: 1.4066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.0000 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 0.0050 chunk 51 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.6165 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= 0.201 Angle : 0.684 7.619 14395 Z= 0.386 Chirality : 0.038 0.185 1666 Planarity : 0.004 0.038 1100 Dihedral : 33.174 174.171 2790 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 0.36 % 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: 1.43 (0.33), residues: 640 helix: 1.73 (0.24), residues: 476 sheet: None (None), residues: 0 loop : -1.41 (0.43), residues: 164 ********************** 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 133 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.804 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2612 time to fit residues: 46.1445 Evaluate side-chains 118 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.046802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.035562 restraints weight = 65505.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.036597 restraints weight = 33138.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037269 restraints weight = 21803.456| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 9999 Z= 0.301 Angle : 0.726 7.535 14395 Z= 0.411 Chirality : 0.040 0.150 1666 Planarity : 0.005 0.037 1100 Dihedral : 33.276 176.234 2790 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.53 % 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: 1.19 (0.33), residues: 640 helix: 1.59 (0.24), residues: 484 sheet: None (None), residues: 0 loop : -1.82 (0.41), residues: 156 =============================================================================== Job complete usr+sys time: 1789.97 seconds wall clock time: 33 minutes 25.79 seconds (2005.79 seconds total)