Starting phenix.real_space_refine on Fri Dec 8 00:01:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jic_22344/12_2023/7jic_22344.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jic_22344/12_2023/7jic_22344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jic_22344/12_2023/7jic_22344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jic_22344/12_2023/7jic_22344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jic_22344/12_2023/7jic_22344.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jic_22344/12_2023/7jic_22344.pdb" } resolution = 3.8 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3770 2.51 5 N 1013 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 163": "NH1" <-> "NH2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1625 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 19, 'TRANS': 208} Chain breaks: 4 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1285 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 4 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "H" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1601 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1469 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.83, per 1000 atoms: 0.64 Number of scatterers: 5980 At special positions: 0 Unit cell: (61.05, 75.075, 170.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1168 8.00 N 1013 7.00 C 3770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 13 sheets defined 24.2% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 293 through 313 Processing helix chain 'B' and resid 10 through 37 Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 58 through 82 Processing helix chain 'B' and resid 90 through 115 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.827A pdb=" N GLN B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.626A pdb=" N ALA B 164 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 224 removed outlier: 3.747A pdb=" N LYS B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET B 224 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.904A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 182 through 186 removed outlier: 3.696A pdb=" N GLU L 186 " --> pdb=" O LYS L 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 182 through 186' Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.863A pdb=" N GLU A 273 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 4.008A pdb=" N ASP A 32 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA A 34 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU A 36 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 247 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 239 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 74 " --> pdb=" O TRP A 81 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 84 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 196 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 190 removed outlier: 7.754A pdb=" N LEU A 188 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR A 112 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET A 190 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN A 114 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N CYS A 97 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 123 removed outlier: 6.066A pdb=" N LEU A 121 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP A 159 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG A 123 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 160 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.513A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.397A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR H 108 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.020A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER H 185 " --> pdb=" O PRO H 173 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL H 187 " --> pdb=" O THR H 171 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR H 171 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR H 189 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL H 169 " --> pdb=" O THR H 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.742A pdb=" N THR H 157 " --> pdb=" O ASN H 205 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.645A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N GLU L 104 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 128 through 135 Processing sheet with id=AB4, first strand: chain 'L' and resid 144 through 149 removed outlier: 3.725A pdb=" N ALA L 192 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS L 193 " --> pdb=" O LYS L 206 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS L 206 " --> pdb=" O CYS L 193 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1948 1.35 - 1.46: 1502 1.46 - 1.58: 2622 1.58 - 1.70: 0 1.70 - 1.81: 41 Bond restraints: 6113 Sorted by residual: bond pdb=" CA ILE A 297 " pdb=" CB ILE A 297 " ideal model delta sigma weight residual 1.540 1.528 0.013 1.25e-02 6.40e+03 1.02e+00 bond pdb=" CA ILE A 306 " pdb=" CB ILE A 306 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.25e-02 6.40e+03 8.84e-01 bond pdb=" CB PRO B 55 " pdb=" CG PRO B 55 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.40e-01 bond pdb=" CA VAL A 304 " pdb=" CB VAL A 304 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.29e-02 6.01e+03 8.24e-01 bond pdb=" CA THR A 292 " pdb=" CB THR A 292 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.70e-02 1.37e+03 7.65e-01 ... (remaining 6108 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 256 107.21 - 113.90: 3440 113.90 - 120.59: 2215 120.59 - 127.29: 2352 127.29 - 133.98: 89 Bond angle restraints: 8352 Sorted by residual: angle pdb=" C THR L 50 " pdb=" CA THR L 50 " pdb=" CB THR L 50 " ideal model delta sigma weight residual 110.42 115.75 -5.33 1.99e+00 2.53e-01 7.18e+00 angle pdb=" N ALA H 16 " pdb=" CA ALA H 16 " pdb=" C ALA H 16 " ideal model delta sigma weight residual 108.34 111.03 -2.69 1.31e+00 5.83e-01 4.22e+00 angle pdb=" N PRO A 203 " pdb=" CA PRO A 203 " pdb=" C PRO A 203 " ideal model delta sigma weight residual 110.70 113.05 -2.35 1.22e+00 6.72e-01 3.70e+00 angle pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 120.60 124.78 -4.18 2.20e+00 2.07e-01 3.62e+00 angle pdb=" CA THR L 50 " pdb=" C THR L 50 " pdb=" N SER L 51 " ideal model delta sigma weight residual 116.84 119.94 -3.10 1.71e+00 3.42e-01 3.29e+00 ... (remaining 8347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.68: 3244 10.68 - 21.36: 230 21.36 - 32.04: 82 32.04 - 42.72: 30 42.72 - 53.40: 6 Dihedral angle restraints: 3592 sinusoidal: 1184 harmonic: 2408 Sorted by residual: dihedral pdb=" SG CYS B 156 " pdb=" CB CYS B 190 " pdb=" SG CYS B 190 " pdb=" CA CYS B 190 " ideal model delta sinusoidal sigma weight residual 79.00 26.09 52.91 1 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CA CYS B 157 " pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " pdb=" SG CYS B 175 " ideal model delta sinusoidal sigma weight residual 183.00 131.19 51.81 1 2.00e+01 2.50e-03 9.16e+00 dihedral pdb=" N LYS L 125 " pdb=" CA LYS L 125 " pdb=" CB LYS L 125 " pdb=" CG LYS L 125 " ideal model delta sinusoidal sigma weight residual -60.00 -103.72 43.72 3 1.50e+01 4.44e-03 7.86e+00 ... (remaining 3589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 591 0.026 - 0.052: 237 0.052 - 0.079: 67 0.079 - 0.105: 42 0.105 - 0.131: 24 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA ILE A 84 " pdb=" N ILE A 84 " pdb=" C ILE A 84 " pdb=" CB ILE A 84 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL H 92 " pdb=" N VAL H 92 " pdb=" C VAL H 92 " pdb=" CB VAL H 92 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA VAL A 202 " pdb=" N VAL A 202 " pdb=" C VAL A 202 " pdb=" CB VAL A 202 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 958 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 203 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 204 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 154 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO H 155 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 202 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 203 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " 0.019 5.00e-02 4.00e+02 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1045 2.77 - 3.30: 5445 3.30 - 3.84: 9764 3.84 - 4.37: 10329 4.37 - 4.90: 18705 Nonbonded interactions: 45288 Sorted by model distance: nonbonded pdb=" OG SER A 53 " pdb=" O SER A 56 " model vdw 2.241 2.440 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 101 " model vdw 2.297 2.440 nonbonded pdb=" O TYR L 185 " pdb=" OH TYR L 191 " model vdw 2.306 2.440 nonbonded pdb=" NE2 GLN A 98 " pdb=" O PRO A 101 " model vdw 2.307 2.520 nonbonded pdb=" O PRO A 203 " pdb=" OG SER A 206 " model vdw 2.310 2.440 ... (remaining 45283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.050 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: 8.620 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.770 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.002 0.046 6113 Z= 0.134 Angle : 0.447 5.334 8352 Z= 0.237 Chirality : 0.038 0.131 961 Planarity : 0.003 0.043 1076 Dihedral : 9.260 53.399 2014 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.97 (0.27), residues: 804 helix: 0.90 (0.34), residues: 196 sheet: -1.81 (0.28), residues: 285 loop : -2.13 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 34 HIS 0.003 0.001 HIS A 216 PHE 0.008 0.001 PHE A 83 TYR 0.007 0.001 TYR H 103 ARG 0.001 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1892 time to fit residues: 42.7318 Evaluate side-chains 87 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8637 ------------------------------------------------------------------------------- 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: 0.3980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.0570 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN H 177 GLN L 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6113 Z= 0.193 Angle : 0.535 6.585 8352 Z= 0.267 Chirality : 0.040 0.142 961 Planarity : 0.004 0.061 1076 Dihedral : 3.296 13.816 865 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Rotamer: Outliers : 2.77 % Allowed : 13.00 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.77 (0.30), residues: 804 helix: 2.65 (0.35), residues: 182 sheet: -1.20 (0.31), residues: 286 loop : -1.63 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 147 HIS 0.004 0.001 HIS A 218 PHE 0.016 0.001 PHE L 208 TYR 0.010 0.001 TYR H 103 ARG 0.002 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.1800 time to fit residues: 26.3925 Evaluate side-chains 92 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0582 time to fit residues: 1.7398 ------------------------------------------------------------------------------- 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: 5.9990 chunk 23 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.089 6113 Z= 0.727 Angle : 0.859 12.299 8352 Z= 0.436 Chirality : 0.048 0.172 961 Planarity : 0.005 0.045 1076 Dihedral : 5.278 24.664 865 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.09 % Favored : 92.66 % Rotamer: Outliers : 3.81 % Allowed : 17.50 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.30), residues: 804 helix: 2.60 (0.35), residues: 196 sheet: -1.27 (0.31), residues: 288 loop : -1.83 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 109 HIS 0.016 0.003 HIS A 218 PHE 0.027 0.003 PHE A 94 TYR 0.027 0.003 TYR H 93 ARG 0.006 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 96 average time/residue: 0.1888 time to fit residues: 23.8169 Evaluate side-chains 78 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0595 time to fit residues: 2.0280 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 36 GLN L 37 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6113 Z= 0.190 Angle : 0.550 6.531 8352 Z= 0.275 Chirality : 0.041 0.157 961 Planarity : 0.004 0.038 1076 Dihedral : 4.104 19.161 865 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.64 % Rotamer: Outliers : 1.91 % Allowed : 17.50 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.31), residues: 804 helix: 3.77 (0.35), residues: 183 sheet: -1.14 (0.32), residues: 281 loop : -1.40 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 147 HIS 0.004 0.001 HIS A 218 PHE 0.011 0.001 PHE A 83 TYR 0.018 0.001 TYR H 151 ARG 0.003 0.000 ARG L 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 94 average time/residue: 0.2073 time to fit residues: 25.0754 Evaluate side-chains 82 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0612 time to fit residues: 1.3919 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 6113 Z= 0.344 Angle : 0.600 7.507 8352 Z= 0.304 Chirality : 0.042 0.151 961 Planarity : 0.004 0.040 1076 Dihedral : 4.263 17.166 865 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 2.25 % Allowed : 19.24 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.12 (0.31), residues: 804 helix: 3.91 (0.35), residues: 184 sheet: -1.10 (0.31), residues: 291 loop : -1.44 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 147 HIS 0.007 0.001 HIS A 218 PHE 0.013 0.001 PHE A 83 TYR 0.015 0.002 TYR A 95 ARG 0.003 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.1875 time to fit residues: 22.1042 Evaluate side-chains 80 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0571 time to fit residues: 1.6793 ------------------------------------------------------------------------------- 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: 0.0270 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6113 Z= 0.244 Angle : 0.568 6.731 8352 Z= 0.286 Chirality : 0.041 0.151 961 Planarity : 0.004 0.040 1076 Dihedral : 4.014 16.647 865 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.61 % Favored : 96.27 % Rotamer: Outliers : 1.73 % Allowed : 18.89 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.07 (0.31), residues: 804 helix: 4.05 (0.35), residues: 184 sheet: -1.01 (0.31), residues: 289 loop : -1.29 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 147 HIS 0.005 0.001 HIS A 218 PHE 0.012 0.001 PHE A 83 TYR 0.011 0.001 TYR H 103 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 88 average time/residue: 0.1930 time to fit residues: 22.3277 Evaluate side-chains 79 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0550 time to fit residues: 1.3380 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.0040 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6113 Z= 0.172 Angle : 0.565 8.114 8352 Z= 0.282 Chirality : 0.041 0.149 961 Planarity : 0.004 0.041 1076 Dihedral : 3.831 16.791 865 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 0.35 % Allowed : 21.14 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.12 (0.31), residues: 804 helix: 4.01 (0.35), residues: 184 sheet: -1.04 (0.31), residues: 288 loop : -1.13 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 147 HIS 0.002 0.001 HIS A 218 PHE 0.011 0.001 PHE A 83 TYR 0.011 0.001 TYR H 103 ARG 0.001 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.1942 time to fit residues: 21.7326 Evaluate side-chains 74 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0860 time to fit residues: 1.0274 ------------------------------------------------------------------------------- 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: 20.0000 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 6113 Z= 0.451 Angle : 0.686 7.946 8352 Z= 0.348 Chirality : 0.044 0.158 961 Planarity : 0.004 0.046 1076 Dihedral : 4.495 17.129 865 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.53 % Rotamer: Outliers : 1.56 % Allowed : 20.28 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.01 (0.31), residues: 804 helix: 3.74 (0.36), residues: 190 sheet: -1.06 (0.33), residues: 274 loop : -1.24 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 33 HIS 0.010 0.002 HIS A 218 PHE 0.016 0.002 PHE A 83 TYR 0.013 0.002 TYR L 85 ARG 0.004 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.1908 time to fit residues: 19.6918 Evaluate side-chains 75 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0594 time to fit residues: 1.6241 ------------------------------------------------------------------------------- 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: 0.0020 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6113 Z= 0.171 Angle : 0.576 7.662 8352 Z= 0.289 Chirality : 0.041 0.153 961 Planarity : 0.004 0.041 1076 Dihedral : 3.924 17.233 865 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.35 % Allowed : 21.14 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.32), residues: 804 helix: 4.07 (0.35), residues: 184 sheet: -0.98 (0.32), residues: 287 loop : -1.07 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 147 HIS 0.005 0.001 HIS A 216 PHE 0.013 0.001 PHE A 83 TYR 0.020 0.001 TYR A 95 ARG 0.002 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 80 average time/residue: 0.2111 time to fit residues: 21.8206 Evaluate side-chains 72 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0542 time to fit residues: 1.0531 ------------------------------------------------------------------------------- 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: 10.0000 chunk 54 optimal weight: 10.0000 chunk 81 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6113 Z= 0.347 Angle : 0.644 6.974 8352 Z= 0.330 Chirality : 0.043 0.151 961 Planarity : 0.004 0.041 1076 Dihedral : 4.258 17.891 865 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.17 % Allowed : 21.66 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.32), residues: 804 helix: 3.79 (0.36), residues: 190 sheet: -1.06 (0.33), residues: 270 loop : -1.10 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 147 HIS 0.008 0.001 HIS A 218 PHE 0.014 0.002 PHE A 83 TYR 0.023 0.002 TYR A 95 ARG 0.003 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1972 time to fit residues: 19.8750 Evaluate side-chains 70 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9592 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.110946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079662 restraints weight = 14299.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082157 restraints weight = 8114.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083811 restraints weight = 5709.550| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6113 Z= 0.214 Angle : 0.607 7.274 8352 Z= 0.305 Chirality : 0.042 0.150 961 Planarity : 0.004 0.041 1076 Dihedral : 4.022 18.027 865 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.17 % Allowed : 22.36 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.17 (0.32), residues: 804 helix: 4.00 (0.35), residues: 184 sheet: -1.10 (0.33), residues: 277 loop : -0.98 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 147 HIS 0.004 0.001 HIS A 216 PHE 0.011 0.001 PHE A 83 TYR 0.019 0.001 TYR A 95 ARG 0.002 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1483.97 seconds wall clock time: 27 minutes 45.04 seconds (1665.04 seconds total)