Starting phenix.real_space_refine (version: dev) on Tue Apr 5 09:51:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhq_12190/04_2022/7bhq_12190.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhq_12190/04_2022/7bhq_12190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhq_12190/04_2022/7bhq_12190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhq_12190/04_2022/7bhq_12190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhq_12190/04_2022/7bhq_12190.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhq_12190/04_2022/7bhq_12190.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7402 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1475 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "B" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1493 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "C" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1458 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "D" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1483 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 194} Chain: "E" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1493 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Time building chain proxies: 4.68, per 1000 atoms: 0.63 Number of scatterers: 7402 At special positions: 0 Unit cell: (106.496, 103.168, 125.632, 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 5 16.00 O 1545 8.00 N 1269 7.00 C 4583 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: 3.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 28.5% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.888A pdb=" N LEU A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 91 removed outlier: 3.546A pdb=" N GLY A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.873A pdb=" N SER B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 40 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 93 removed outlier: 3.797A pdb=" N THR B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR B 60 " --> pdb=" O ASN B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.949A pdb=" N LEU C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 40 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 93 removed outlier: 3.551A pdb=" N ALA C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'D' and resid 32 through 44 removed outlier: 4.375A pdb=" N LEU D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 59 through 73 removed outlier: 3.533A pdb=" N ALA D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 95 removed outlier: 3.551A pdb=" N GLY D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 46 removed outlier: 4.053A pdb=" N LEU E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 removed outlier: 4.276A pdb=" N THR E 59 " --> pdb=" O ASN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 90 removed outlier: 3.589A pdb=" N SER E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 95 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 163 removed outlier: 4.050A pdb=" N GLY A 126 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 128 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 196 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 230 " --> pdb=" O MET A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.318A pdb=" N ALA A 186 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 207 Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 163 removed outlier: 3.946A pdb=" N GLY B 100 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 230 " --> pdb=" O MET B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.668A pdb=" N LYS B 135 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 149 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.532A pdb=" N ALA B 186 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 222 through 223 removed outlier: 3.794A pdb=" N GLY B 205 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 206 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 104 Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.035A pdb=" N ALA C 186 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 191 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AB4, first strand: chain 'D' and resid 121 through 122 removed outlier: 3.588A pdb=" N GLY D 111 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 121 through 122 removed outlier: 3.588A pdb=" N GLY D 111 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA D 186 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AB7, first strand: chain 'E' and resid 121 through 122 removed outlier: 3.572A pdb=" N SER E 121 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY E 111 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA E 138 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR E 150 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE E 140 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 121 through 122 removed outlier: 3.572A pdb=" N SER E 121 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY E 111 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 205 through 208 421 hydrogen bonds defined for protein. 1116 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: 2.37 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2389 1.33 - 1.45: 730 1.45 - 1.57: 4353 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 7482 Sorted by residual: bond pdb=" C ASN D 51 " pdb=" O ASN D 51 " ideal model delta sigma weight residual 1.233 1.239 -0.006 4.80e-03 4.34e+04 1.47e+00 bond pdb=" C SER D 35 " pdb=" N PHE D 36 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.40e-02 5.10e+03 1.46e+00 bond pdb=" CG GLN D 89 " pdb=" CD GLN D 89 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB PRO C 176 " pdb=" CG PRO C 176 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.92e-01 bond pdb=" CB ASN C 46 " pdb=" CG ASN C 46 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.70e-01 ... (remaining 7477 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 182 107.29 - 113.97: 4565 113.97 - 120.65: 2735 120.65 - 127.33: 2679 127.33 - 134.00: 52 Bond angle restraints: 10213 Sorted by residual: angle pdb=" CA ASN D 51 " pdb=" C ASN D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 118.16 120.49 -2.33 7.00e-01 2.04e+00 1.10e+01 angle pdb=" C ASN D 51 " pdb=" CA ASN D 51 " pdb=" CB ASN D 51 " ideal model delta sigma weight residual 110.71 107.77 2.94 9.40e-01 1.13e+00 9.81e+00 angle pdb=" N GLN D 89 " pdb=" CA GLN D 89 " pdb=" CB GLN D 89 " ideal model delta sigma weight residual 110.12 114.60 -4.48 1.47e+00 4.63e-01 9.29e+00 angle pdb=" N VAL D 148 " pdb=" CA VAL D 148 " pdb=" C VAL D 148 " ideal model delta sigma weight residual 111.81 109.25 2.56 8.60e-01 1.35e+00 8.87e+00 angle pdb=" C ASN D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta sigma weight residual 121.65 118.83 2.82 1.01e+00 9.80e-01 7.78e+00 ... (remaining 10208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4126 17.90 - 35.81: 257 35.81 - 53.71: 51 53.71 - 71.62: 19 71.62 - 89.52: 13 Dihedral angle restraints: 4466 sinusoidal: 1661 harmonic: 2805 Sorted by residual: dihedral pdb=" CA ASN D 51 " pdb=" C ASN D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL D 41 " pdb=" C VAL D 41 " pdb=" N ALA D 42 " pdb=" CA ALA D 42 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO D 52 " pdb=" C PRO D 52 " pdb=" N LEU D 53 " pdb=" CA LEU D 53 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 774 0.028 - 0.055: 318 0.055 - 0.083: 121 0.083 - 0.110: 62 0.110 - 0.138: 19 Chirality restraints: 1294 Sorted by residual: chirality pdb=" CA VAL B 103 " pdb=" N VAL B 103 " pdb=" C VAL B 103 " pdb=" CB VAL B 103 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CG LEU C 53 " pdb=" CB LEU C 53 " pdb=" CD1 LEU C 53 " pdb=" CD2 LEU C 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE E 108 " pdb=" N ILE E 108 " pdb=" C ILE E 108 " pdb=" CB ILE E 108 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1291 not shown) Planarity restraints: 1337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO D 49 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 48 " 0.022 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO E 49 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " -0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 124 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.016 5.00e-02 4.00e+02 ... (remaining 1334 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 299 2.71 - 3.26: 7794 3.26 - 3.81: 12437 3.81 - 4.35: 15053 4.35 - 4.90: 25227 Nonbonded interactions: 60810 Sorted by model distance: nonbonded pdb=" O PRO A 176 " pdb=" OH TYR A 180 " model vdw 2.168 2.440 nonbonded pdb=" O SER D 34 " pdb=" OG1 THR D 38 " model vdw 2.169 2.440 nonbonded pdb=" O PRO D 176 " pdb=" OH TYR D 180 " model vdw 2.190 2.440 nonbonded pdb=" O PRO E 176 " pdb=" OH TYR E 180 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR A 137 " pdb=" OG1 THR A 185 " model vdw 2.238 2.440 ... (remaining 60805 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' and resid 34 through 232) selection = (chain 'B' and resid 34 through 232) selection = chain 'C' selection = (chain 'D' and resid 34 through 232) selection = (chain 'E' and resid 34 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 4583 2.51 5 N 1269 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 40.690 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: 106.900 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.000 Process input model: 27.500 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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: 178.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4647 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7482 Z= 0.189 Angle : 0.496 5.839 10213 Z= 0.274 Chirality : 0.040 0.138 1294 Planarity : 0.003 0.052 1337 Dihedral : 14.118 89.520 2676 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1000 helix: 1.04 (0.34), residues: 261 sheet: 0.87 (0.32), residues: 284 loop : 0.51 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1743 time to fit residues: 31.2923 Evaluate side-chains 35 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 204 GLN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN C 64 GLN C 130 GLN C 169 GLN C 230 GLN D 92 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4719 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 7482 Z= 0.249 Angle : 0.623 7.741 10213 Z= 0.326 Chirality : 0.044 0.207 1294 Planarity : 0.005 0.080 1337 Dihedral : 4.949 40.001 1040 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 0.93 (0.27), residues: 1000 helix: 1.32 (0.34), residues: 263 sheet: 0.67 (0.34), residues: 259 loop : 0.33 (0.29), residues: 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.1753 time to fit residues: 18.7341 Evaluate side-chains 48 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0853 time to fit residues: 2.9064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 30.0000 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.0070 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4673 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 7482 Z= 0.150 Angle : 0.517 12.102 10213 Z= 0.267 Chirality : 0.040 0.174 1294 Planarity : 0.004 0.050 1337 Dihedral : 4.589 36.629 1040 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.10 % 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: 1.18 (0.28), residues: 1000 helix: 1.91 (0.35), residues: 257 sheet: 0.72 (0.33), residues: 275 loop : 0.30 (0.29), residues: 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 49 average time/residue: 0.1960 time to fit residues: 14.0273 Evaluate side-chains 36 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0693 time to fit residues: 1.5121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 46 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7482 Z= 0.200 Angle : 0.597 14.316 10213 Z= 0.309 Chirality : 0.042 0.188 1294 Planarity : 0.004 0.055 1337 Dihedral : 4.981 41.037 1040 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 2.07 % 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: 0.85 (0.27), residues: 1000 helix: 1.73 (0.34), residues: 257 sheet: 0.73 (0.33), residues: 277 loop : -0.14 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 0.1996 time to fit residues: 16.9415 Evaluate side-chains 43 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0676 time to fit residues: 2.3894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 0.0060 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 0.0050 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4699 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 7482 Z= 0.152 Angle : 0.540 17.229 10213 Z= 0.279 Chirality : 0.040 0.176 1294 Planarity : 0.004 0.051 1337 Dihedral : 4.749 44.319 1040 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.85 % 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: 0.97 (0.27), residues: 1000 helix: 1.94 (0.34), residues: 263 sheet: 0.74 (0.33), residues: 271 loop : -0.11 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.1902 time to fit residues: 13.4657 Evaluate side-chains 41 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1226 time to fit residues: 2.0710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.0270 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 75 ASN A 230 GLN D 33 GLN E 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4728 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 7482 Z= 0.205 Angle : 0.584 18.220 10213 Z= 0.309 Chirality : 0.041 0.182 1294 Planarity : 0.004 0.053 1337 Dihedral : 4.892 44.849 1040 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.85 % 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: 0.89 (0.27), residues: 1000 helix: 2.00 (0.34), residues: 263 sheet: 0.74 (0.33), residues: 282 loop : -0.32 (0.28), residues: 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.2040 time to fit residues: 14.3540 Evaluate side-chains 36 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0691 time to fit residues: 1.7195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 80 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4706 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.319 7482 Z= 0.315 Angle : 0.617 29.084 10213 Z= 0.344 Chirality : 0.040 0.175 1294 Planarity : 0.004 0.072 1337 Dihedral : 4.746 44.358 1040 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.61 % 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: 1.11 (0.28), residues: 1000 helix: 2.23 (0.34), residues: 263 sheet: 0.77 (0.33), residues: 295 loop : -0.15 (0.29), residues: 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 46 average time/residue: 0.2091 time to fit residues: 13.7786 Evaluate side-chains 40 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0692 time to fit residues: 1.3208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4770 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 7482 Z= 0.229 Angle : 0.648 17.210 10213 Z= 0.340 Chirality : 0.043 0.181 1294 Planarity : 0.004 0.055 1337 Dihedral : 5.355 44.204 1040 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.85 % 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: 0.59 (0.28), residues: 1000 helix: 1.67 (0.34), residues: 269 sheet: 0.38 (0.31), residues: 311 loop : -0.37 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.861 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.2099 time to fit residues: 15.0549 Evaluate side-chains 45 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0699 time to fit residues: 1.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.0270 overall best weight: 3.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4772 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 1.031 7482 Z= 1.096 Angle : 1.098 81.934 10213 Z= 0.496 Chirality : 0.043 0.189 1294 Planarity : 0.005 0.089 1337 Dihedral : 5.457 43.894 1040 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.11 % 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: 0.37 (0.27), residues: 1000 helix: 1.58 (0.34), residues: 269 sheet: 0.19 (0.32), residues: 296 loop : -0.49 (0.29), residues: 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.799 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.2101 time to fit residues: 14.1230 Evaluate side-chains 43 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0674 time to fit residues: 1.4759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4751 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 1.060 7482 Z= 1.104 Angle : 1.020 76.557 10213 Z= 0.458 Chirality : 0.041 0.199 1294 Planarity : 0.004 0.054 1337 Dihedral : 5.232 44.875 1040 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.11 % 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: 0.59 (0.28), residues: 1000 helix: 1.80 (0.34), residues: 269 sheet: 0.27 (0.31), residues: 308 loop : -0.36 (0.30), residues: 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.931 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.1888 time to fit residues: 14.2154 Evaluate side-chains 44 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0663 time to fit residues: 1.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.0040 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.1154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.177746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.140805 restraints weight = 27050.620| |-----------------------------------------------------------------------------| r_work (start): 0.4628 rms_B_bonded: 6.25 r_work: 0.4590 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work: 0.4587 rms_B_bonded: 5.59 restraints_weight: 4.0000 r_work: 0.4588 rms_B_bonded: 5.05 restraints_weight: 8.0000 r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.020 1.093 7482 Z= 1.522 Angle : 1.583 106.073 10213 Z= 0.662 Chirality : 0.046 0.551 1294 Planarity : 0.004 0.054 1337 Dihedral : 5.226 44.865 1040 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.11 % 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: 0.60 (0.28), residues: 1000 helix: 1.80 (0.34), residues: 269 sheet: 0.27 (0.31), residues: 308 loop : -0.34 (0.30), residues: 423 =============================================================================== Job complete usr+sys time: 2746.42 seconds wall clock time: 52 minutes 18.52 seconds (3138.52 seconds total)