Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 11:25:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/10_2023/7crb_30449.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/10_2023/7crb_30449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/10_2023/7crb_30449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/10_2023/7crb_30449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/10_2023/7crb_30449.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7crb_30449/10_2023/7crb_30449.pdb" } resolution = 3.16 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= -0.000 sd= 1.000 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 39 5.16 5 C 4318 2.51 5 N 1155 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 117": "OE1" <-> "OE2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J GLU 221": "OE1" <-> "OE2" Residue "J GLU 249": "OE1" <-> "OE2" Residue "J GLU 270": "OE1" <-> "OE2" Residue "J ARG 271": "NH1" <-> "NH2" Residue "J GLU 299": "OE1" <-> "OE2" Residue "J GLU 300": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ARG 937": "NH1" <-> "NH2" Residue "A GLU 965": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A GLU 1133": "OE1" <-> "OE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A GLU 1167": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 6806 Number of models: 1 Model: "" Number of chains: 2 Chain: "J" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1880 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "A" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4926 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 27, 'TRANS': 588} Time building chain proxies: 4.32, per 1000 atoms: 0.63 Number of scatterers: 6806 At special positions: 0 Unit cell: (84.5383, 114.182, 93.3215, 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 39 16.00 O 1294 8.00 N 1155 7.00 C 4318 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 31.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'J' and resid 68 through 84 removed outlier: 4.227A pdb=" N SER J 84 " --> pdb=" O HIS J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 102 removed outlier: 4.607A pdb=" N VAL J 95 " --> pdb=" O MET J 91 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.531A pdb=" N ALA J 129 " --> pdb=" O THR J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 157 through 177 Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 194 through 197 Processing helix chain 'J' and resid 198 through 210 removed outlier: 4.319A pdb=" N PHE J 204 " --> pdb=" O THR J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 223 Processing helix chain 'J' and resid 226 through 239 removed outlier: 3.674A pdb=" N GLU J 239 " --> pdb=" O LEU J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 244 through 261 Processing helix chain 'J' and resid 268 through 277 Processing helix chain 'J' and resid 302 through 309 removed outlier: 3.877A pdb=" N TYR J 309 " --> pdb=" O TYR J 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.618A pdb=" N SER A 600 " --> pdb=" O THR A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 removed outlier: 3.671A pdb=" N LEU A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 620 through 626' Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.616A pdb=" N GLN A 647 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 745 removed outlier: 3.919A pdb=" N GLU A 743 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 Processing helix chain 'A' and resid 858 through 862 Processing helix chain 'A' and resid 880 through 886 removed outlier: 3.732A pdb=" N ILE A 883 " --> pdb=" O PRO A 880 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 884 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 953 removed outlier: 3.889A pdb=" N ILE A 950 " --> pdb=" O PRO A 947 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 removed outlier: 4.097A pdb=" N LYS A 968 " --> pdb=" O GLU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 removed outlier: 3.609A pdb=" N LEU A 974 " --> pdb=" O PHE A 970 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 975' Processing helix chain 'A' and resid 990 through 996 removed outlier: 3.652A pdb=" N LYS A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1064 Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 585 removed outlier: 3.513A pdb=" N GLY A 585 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 680 through 682 removed outlier: 6.400A pdb=" N LEU A 681 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N MET A 704 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 797 " --> pdb=" O ASN A 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 788 through 789 removed outlier: 3.583A pdb=" N ILE A 789 " --> pdb=" O ALA A 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 843 through 845 removed outlier: 3.530A pdb=" N ILE A 939 " --> pdb=" O LEU A 917 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.707A pdb=" N LEU A 980 " --> pdb=" O ARG A1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1012 through 1013 Processing sheet with id=AA7, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 3.653A pdb=" N VAL A1129 " --> pdb=" O GLU A1176 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A1130 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A1137 " --> pdb=" O ASP A1132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 3.653A pdb=" N VAL A1129 " --> pdb=" O GLU A1176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1164 216 hydrogen bonds defined for protein. 585 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: 2.01 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1139 1.31 - 1.43: 1761 1.43 - 1.56: 3987 1.56 - 1.68: 0 1.68 - 1.81: 53 Bond restraints: 6940 Sorted by residual: bond pdb=" C PRO A 947 " pdb=" O PRO A 947 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.18e-02 7.18e+03 1.71e+01 bond pdb=" CA SER J 296 " pdb=" CB SER J 296 " ideal model delta sigma weight residual 1.531 1.467 0.063 1.62e-02 3.81e+03 1.54e+01 bond pdb=" N LEU A1121 " pdb=" CA LEU A1121 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.33e+00 bond pdb=" N LYS A1122 " pdb=" CA LYS A1122 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.31e+00 bond pdb=" N VAL A1113 " pdb=" CA VAL A1113 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.04e+00 ... (remaining 6935 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 162 105.94 - 112.97: 3809 112.97 - 119.99: 2403 119.99 - 127.01: 2950 127.01 - 134.03: 77 Bond angle restraints: 9401 Sorted by residual: angle pdb=" N SER J 294 " pdb=" CA SER J 294 " pdb=" C SER J 294 " ideal model delta sigma weight residual 113.38 102.25 11.13 1.23e+00 6.61e-01 8.19e+01 angle pdb=" C PRO A 947 " pdb=" CA PRO A 947 " pdb=" CB PRO A 947 " ideal model delta sigma weight residual 110.95 103.18 7.77 1.31e+00 5.83e-01 3.52e+01 angle pdb=" N GLU J 300 " pdb=" CA GLU J 300 " pdb=" C GLU J 300 " ideal model delta sigma weight residual 111.14 105.10 6.04 1.08e+00 8.57e-01 3.13e+01 angle pdb=" N LEU J 301 " pdb=" CA LEU J 301 " pdb=" C LEU J 301 " ideal model delta sigma weight residual 112.92 106.21 6.71 1.23e+00 6.61e-01 2.97e+01 angle pdb=" CA PRO J 265 " pdb=" N PRO J 265 " pdb=" CD PRO J 265 " ideal model delta sigma weight residual 112.00 104.54 7.46 1.40e+00 5.10e-01 2.84e+01 ... (remaining 9396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 3817 16.76 - 33.52: 364 33.52 - 50.27: 57 50.27 - 67.03: 15 67.03 - 83.79: 8 Dihedral angle restraints: 4261 sinusoidal: 1737 harmonic: 2524 Sorted by residual: dihedral pdb=" N LEU J 295 " pdb=" C LEU J 295 " pdb=" CA LEU J 295 " pdb=" CB LEU J 295 " ideal model delta harmonic sigma weight residual 122.80 110.43 12.37 0 2.50e+00 1.60e-01 2.45e+01 dihedral pdb=" CA LEU A 753 " pdb=" C LEU A 753 " pdb=" N HIS A 754 " pdb=" CA HIS A 754 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C PRO A 947 " pdb=" N PRO A 947 " pdb=" CA PRO A 947 " pdb=" CB PRO A 947 " ideal model delta harmonic sigma weight residual -120.70 -110.26 -10.44 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 4258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 970 0.077 - 0.153: 102 0.153 - 0.230: 10 0.230 - 0.307: 2 0.307 - 0.384: 1 Chirality restraints: 1085 Sorted by residual: chirality pdb=" CA LEU J 295 " pdb=" N LEU J 295 " pdb=" C LEU J 295 " pdb=" CB LEU J 295 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA GLN J 297 " pdb=" N GLN J 297 " pdb=" C GLN J 297 " pdb=" CB GLN J 297 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ILE J 298 " pdb=" N ILE J 298 " pdb=" C ILE J 298 " pdb=" CB ILE J 298 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1082 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 98 " 0.021 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP J 98 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP J 98 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP J 98 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 98 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 98 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J 98 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 298 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C ILE J 298 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE J 298 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU J 299 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 300 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" C GLU J 300 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU J 300 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU J 301 " -0.017 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1933 2.81 - 3.33: 6277 3.33 - 3.86: 10539 3.86 - 4.38: 12704 4.38 - 4.90: 21856 Nonbonded interactions: 53309 Sorted by model distance: nonbonded pdb=" O SER A 949 " pdb=" OG SER A 952 " model vdw 2.288 2.440 nonbonded pdb=" NZ LYS A 690 " pdb=" OE2 GLU A 693 " model vdw 2.299 2.520 nonbonded pdb=" O LEU A1060 " pdb=" OG1 THR A1064 " model vdw 2.311 2.440 nonbonded pdb=" NH1 ARG J 151 " pdb=" OE1 GLU J 167 " model vdw 2.337 2.520 nonbonded pdb=" N SER J 294 " pdb=" N LEU J 295 " model vdw 2.352 2.560 ... (remaining 53304 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=0.43 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.450 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.130 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.005 0.063 6940 Z= 0.349 Angle : 0.809 11.134 9401 Z= 0.491 Chirality : 0.052 0.384 1085 Planarity : 0.004 0.035 1198 Dihedral : 13.844 83.788 2611 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.77 % Allowed : 0.89 % Favored : 98.34 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.29), residues: 845 helix: -0.88 (0.32), residues: 238 sheet: -2.37 (0.42), residues: 162 loop : -1.47 (0.31), residues: 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.780 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 0.1766 time to fit residues: 21.1820 Evaluate side-chains 67 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0760 time to fit residues: 1.5771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6940 Z= 0.310 Angle : 0.639 9.769 9401 Z= 0.332 Chirality : 0.044 0.153 1085 Planarity : 0.004 0.043 1198 Dihedral : 5.159 21.690 915 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 1.66 % Allowed : 7.41 % Favored : 90.93 % 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: -1.94 (0.30), residues: 845 helix: -0.32 (0.34), residues: 246 sheet: -2.19 (0.42), residues: 162 loop : -1.44 (0.31), residues: 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.819 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.1747 time to fit residues: 19.6020 Evaluate side-chains 74 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0672 time to fit residues: 2.3427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6940 Z= 0.315 Angle : 0.623 9.143 9401 Z= 0.321 Chirality : 0.044 0.154 1085 Planarity : 0.004 0.040 1198 Dihedral : 5.086 21.630 915 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.66 % Allowed : 8.81 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.30), residues: 845 helix: 0.02 (0.34), residues: 239 sheet: -2.10 (0.43), residues: 158 loop : -1.37 (0.31), residues: 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.794 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.2095 time to fit residues: 23.5585 Evaluate side-chains 70 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0672 time to fit residues: 2.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN J 277 GLN A 643 HIS A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6940 Z= 0.225 Angle : 0.574 9.290 9401 Z= 0.294 Chirality : 0.043 0.156 1085 Planarity : 0.003 0.033 1198 Dihedral : 4.822 20.166 915 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.79 % Allowed : 9.45 % Favored : 88.76 % 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: -1.36 (0.31), residues: 845 helix: 0.41 (0.36), residues: 230 sheet: -2.03 (0.44), residues: 157 loop : -1.12 (0.31), residues: 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.824 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 82 average time/residue: 0.1992 time to fit residues: 22.3975 Evaluate side-chains 71 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0664 time to fit residues: 1.7245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 149 HIS J 261 GLN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6940 Z= 0.319 Angle : 0.621 10.401 9401 Z= 0.317 Chirality : 0.044 0.170 1085 Planarity : 0.004 0.040 1198 Dihedral : 4.969 21.868 915 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.04 % Allowed : 11.37 % Favored : 86.59 % 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: -1.44 (0.31), residues: 845 helix: 0.41 (0.35), residues: 234 sheet: -2.10 (0.43), residues: 159 loop : -1.21 (0.31), residues: 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.782 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 78 average time/residue: 0.2071 time to fit residues: 22.1246 Evaluate side-chains 72 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0989 time to fit residues: 2.4162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 81 optimal weight: 0.0000 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN A1140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6940 Z= 0.207 Angle : 0.557 10.752 9401 Z= 0.284 Chirality : 0.042 0.166 1085 Planarity : 0.003 0.036 1198 Dihedral : 4.673 19.678 915 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.66 % Allowed : 11.49 % Favored : 86.85 % 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: -1.32 (0.31), residues: 845 helix: 0.48 (0.36), residues: 237 sheet: -2.05 (0.43), residues: 158 loop : -1.12 (0.32), residues: 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.750 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 0.1998 time to fit residues: 23.4063 Evaluate side-chains 72 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0768 time to fit residues: 1.9049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 GLN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6940 Z= 0.260 Angle : 0.592 10.798 9401 Z= 0.302 Chirality : 0.043 0.172 1085 Planarity : 0.003 0.040 1198 Dihedral : 4.787 20.972 915 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.28 % Allowed : 13.41 % Favored : 85.31 % 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: -1.32 (0.31), residues: 845 helix: 0.48 (0.35), residues: 237 sheet: -2.12 (0.42), residues: 159 loop : -1.08 (0.32), residues: 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.845 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.2048 time to fit residues: 21.9677 Evaluate side-chains 74 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.742 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0721 time to fit residues: 1.8138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 51 optimal weight: 0.0970 chunk 55 optimal weight: 0.0170 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN A1140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6940 Z= 0.211 Angle : 0.561 11.092 9401 Z= 0.286 Chirality : 0.042 0.170 1085 Planarity : 0.003 0.040 1198 Dihedral : 4.623 19.691 915 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.89 % Allowed : 13.92 % Favored : 85.19 % 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: -1.13 (0.31), residues: 845 helix: 0.70 (0.36), residues: 230 sheet: -2.09 (0.42), residues: 158 loop : -0.95 (0.32), residues: 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.821 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 78 average time/residue: 0.2107 time to fit residues: 22.2938 Evaluate side-chains 71 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0784 time to fit residues: 1.5302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 68 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6940 Z= 0.239 Angle : 0.588 10.980 9401 Z= 0.299 Chirality : 0.043 0.173 1085 Planarity : 0.003 0.041 1198 Dihedral : 4.670 20.497 915 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.38 % Allowed : 14.69 % Favored : 84.93 % 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: -1.27 (0.31), residues: 845 helix: 0.54 (0.36), residues: 238 sheet: -2.11 (0.42), residues: 158 loop : -1.06 (0.32), residues: 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.987 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 0.2145 time to fit residues: 21.3238 Evaluate side-chains 71 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0669 time to fit residues: 1.2885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.0050 chunk 77 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6940 Z= 0.204 Angle : 0.566 10.946 9401 Z= 0.287 Chirality : 0.043 0.287 1085 Planarity : 0.003 0.041 1198 Dihedral : 4.552 19.379 915 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.13 % Allowed : 14.94 % Favored : 84.93 % 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: -1.13 (0.31), residues: 845 helix: 0.72 (0.36), residues: 232 sheet: -2.12 (0.42), residues: 158 loop : -0.95 (0.32), residues: 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.773 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.2196 time to fit residues: 21.2820 Evaluate side-chains 69 residues out of total 783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 916 ASN A1006 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121725 restraints weight = 8369.382| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.63 r_work: 0.3434 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6940 Z= 0.217 Angle : 0.580 11.139 9401 Z= 0.294 Chirality : 0.043 0.298 1085 Planarity : 0.003 0.041 1198 Dihedral : 4.581 19.900 915 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.13 % Allowed : 14.94 % Favored : 84.93 % 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: -1.12 (0.31), residues: 845 helix: 0.74 (0.36), residues: 232 sheet: -2.14 (0.42), residues: 158 loop : -0.95 (0.32), residues: 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.91 seconds wall clock time: 34 minutes 6.91 seconds (2046.91 seconds total)