Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 23:10:22 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/12_2021/6ni2_9375_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/12_2021/6ni2_9375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/12_2021/6ni2_9375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/12_2021/6ni2_9375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/12_2021/6ni2_9375_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ni2_9375/12_2021/6ni2_9375_updated.pdb" } resolution = 4.0 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 5381 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 865 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2699 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 26, 'TRANS': 325, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 72 Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'CIS': 1, 'TRANS': 113} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 100, 'PCIS': 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 109 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.09, per 1000 atoms: 0.57 Number of scatterers: 5381 At special positions: 0 Unit cell: (95.68, 91.52, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 6 15.00 O 1042 8.00 N 910 7.00 C 3402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 767.4 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 3 helices and 14 sheets defined 2.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 17 through 23 removed outlier: 3.728A pdb=" N MET A 82 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 9 through 12 Processing sheet with id= C, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.753A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 74 through 78 removed outlier: 3.572A pdb=" N PHE B 75 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 168 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 164 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= F, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.680A pdb=" N HIS B 198 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 274 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 272 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 218 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 270 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 220 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 268 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 346 through 349 removed outlier: 4.629A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.810A pdb=" N PHE B 87 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 55 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 57 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 83 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS B 59 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 81 " --> pdb=" O CYS B 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.557A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 117 through 119 removed outlier: 6.349A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 100 through 102 removed outlier: 4.257A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= M, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.272A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.847A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1685 1.34 - 1.46: 1215 1.46 - 1.58: 2547 1.58 - 1.70: 22 1.70 - 1.82: 28 Bond restraints: 5497 Sorted by residual: bond pdb=" O1P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.480 1.610 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" O3P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.610 1.482 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C GLN L 39 " pdb=" N LYS L 40 " ideal model delta sigma weight residual 1.339 1.219 0.121 5.57e-02 3.22e+02 4.69e+00 bond pdb=" C ALA A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.334 1.377 -0.044 2.34e-02 1.83e+03 3.46e+00 bond pdb=" CB GLN B 172 " pdb=" CG GLN B 172 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.25e+00 ... (remaining 5492 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.15: 124 105.15 - 112.42: 2796 112.42 - 119.69: 1867 119.69 - 126.95: 2634 126.95 - 134.22: 67 Bond angle restraints: 7488 Sorted by residual: angle pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" C GLU B 156 " ideal model delta sigma weight residual 110.24 117.78 -7.54 1.41e+00 5.03e-01 2.86e+01 angle pdb=" C THR B 74 " pdb=" N PHE B 75 " pdb=" CA PHE B 75 " ideal model delta sigma weight residual 122.29 130.49 -8.20 1.65e+00 3.67e-01 2.47e+01 angle pdb=" C GLN B 189 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " ideal model delta sigma weight residual 122.07 112.79 9.28 2.01e+00 2.48e-01 2.13e+01 angle pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " pdb=" CG LEU A 85 " ideal model delta sigma weight residual 116.30 100.64 15.66 3.50e+00 8.16e-02 2.00e+01 angle pdb=" CB TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 106.79 119.82 -13.03 3.00e+00 1.11e-01 1.89e+01 ... (remaining 7483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.17: 3249 28.17 - 56.34: 35 56.34 - 84.52: 4 84.52 - 112.69: 0 112.69 - 140.86: 1 Dihedral angle restraints: 3289 sinusoidal: 1243 harmonic: 2046 Sorted by residual: dihedral pdb=" CA ALA A 51 " pdb=" C ALA A 51 " pdb=" N THR A 52 " pdb=" CA THR A 52 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA TYR A 59 " pdb=" C TYR A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 3286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 641 0.077 - 0.154: 187 0.154 - 0.231: 23 0.231 - 0.308: 3 0.308 - 0.385: 2 Chirality restraints: 856 Sorted by residual: chirality pdb=" CB VAL B 164 " pdb=" CA VAL B 164 " pdb=" CG1 VAL B 164 " pdb=" CG2 VAL B 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB TPO V 359 " pdb=" CA TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" CG2 TPO V 359 " both_signs ideal model delta sigma weight residual False 2.56 2.26 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 853 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 9 " 0.028 2.00e-02 2.50e+03 2.35e-02 9.65e+00 pdb=" CG PHE B 9 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 113 " 0.022 2.00e-02 2.50e+03 2.04e-02 8.32e+00 pdb=" CG TYR B 113 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 113 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 113 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 113 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 113 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 113 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 21 " 0.019 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR B 21 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 21 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 21 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 21 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 21 " -0.005 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1070 2.78 - 3.31: 4517 3.31 - 3.84: 8675 3.84 - 4.37: 9386 4.37 - 4.90: 16519 Nonbonded interactions: 40167 Sorted by model distance: nonbonded pdb=" OD1 ASP B 204 " pdb=" OH TYR B 208 " model vdw 2.245 2.440 nonbonded pdb=" O ASP A 89 " pdb=" OH TYR A 93 " model vdw 2.256 2.440 nonbonded pdb=" OG SEP V 363 " pdb=" N SEP V 364 " model vdw 2.314 2.520 nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.318 2.440 nonbonded pdb=" OD1 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.337 2.440 ... (remaining 40162 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 21 5.16 5 C 3402 2.51 5 N 910 2.21 5 O 1042 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 group one per residue Write .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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.320 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 16.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.009 0.130 5497 Z= 0.615 Angle : 1.300 15.660 7488 Z= 0.723 Chirality : 0.071 0.385 856 Planarity : 0.007 0.055 951 Dihedral : 10.246 140.860 1971 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.50 (0.31), residues: 682 helix: -0.31 (1.30), residues: 12 sheet: -0.88 (0.30), residues: 271 loop : -1.06 (0.30), residues: 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2006 time to fit residues: 37.9876 Evaluate side-chains 67 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 81 GLN B 85 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 5497 Z= 0.298 Angle : 0.769 9.371 7488 Z= 0.396 Chirality : 0.047 0.218 856 Planarity : 0.007 0.119 951 Dihedral : 8.845 136.974 784 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.56 (0.32), residues: 682 helix: 0.28 (1.45), residues: 12 sheet: -0.04 (0.31), residues: 278 loop : -0.58 (0.31), residues: 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 0.1754 time to fit residues: 23.0274 Evaluate side-chains 72 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0516 time to fit residues: 1.8957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 5497 Z= 0.226 Angle : 0.687 10.928 7488 Z= 0.345 Chirality : 0.045 0.221 856 Planarity : 0.006 0.094 951 Dihedral : 8.560 138.006 784 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.32), residues: 682 helix: 1.13 (1.56), residues: 12 sheet: 0.29 (0.31), residues: 286 loop : -0.41 (0.32), residues: 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 89 average time/residue: 0.1654 time to fit residues: 19.5224 Evaluate side-chains 69 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0506 time to fit residues: 1.3398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.0070 chunk 6 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 62 optimal weight: 9.9990 chunk 65 optimal weight: 0.0670 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 0.0070 chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 overall best weight: 0.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.101 5497 Z= 0.199 Angle : 0.665 11.341 7488 Z= 0.324 Chirality : 0.046 0.243 856 Planarity : 0.006 0.093 951 Dihedral : 8.415 139.517 784 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.02 (0.32), residues: 682 helix: 1.74 (1.64), residues: 12 sheet: 0.62 (0.32), residues: 263 loop : -0.47 (0.31), residues: 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.663 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 94 average time/residue: 0.1579 time to fit residues: 19.8720 Evaluate side-chains 69 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0514 time to fit residues: 1.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 5497 Z= 0.297 Angle : 0.709 9.231 7488 Z= 0.357 Chirality : 0.045 0.223 856 Planarity : 0.007 0.093 951 Dihedral : 8.447 137.693 784 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.02 (0.32), residues: 682 helix: 1.79 (1.61), residues: 12 sheet: 0.56 (0.32), residues: 273 loop : -0.46 (0.31), residues: 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 77 average time/residue: 0.1766 time to fit residues: 18.0730 Evaluate side-chains 72 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0526 time to fit residues: 1.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.0030 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 5497 Z= 0.327 Angle : 0.736 9.199 7488 Z= 0.372 Chirality : 0.046 0.221 856 Planarity : 0.007 0.105 951 Dihedral : 8.697 137.390 784 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: -0.11 (0.33), residues: 682 helix: 1.59 (1.53), residues: 12 sheet: 0.50 (0.32), residues: 283 loop : -0.54 (0.32), residues: 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.1607 time to fit residues: 17.4705 Evaluate side-chains 73 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0501 time to fit residues: 1.6056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.0270 chunk 65 optimal weight: 0.0770 chunk 41 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.117 5497 Z= 0.212 Angle : 0.678 10.246 7488 Z= 0.329 Chirality : 0.045 0.218 856 Planarity : 0.006 0.114 951 Dihedral : 8.518 139.833 784 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.33), residues: 682 helix: 1.98 (1.63), residues: 12 sheet: 0.87 (0.32), residues: 272 loop : -0.42 (0.31), residues: 398 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 0.1832 time to fit residues: 17.5965 Evaluate side-chains 67 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0540 time to fit residues: 1.0068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 57 optimal weight: 0.0670 chunk 61 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.133 5497 Z= 0.248 Angle : 0.698 11.128 7488 Z= 0.346 Chirality : 0.044 0.219 856 Planarity : 0.007 0.120 951 Dihedral : 8.445 139.288 784 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.33), residues: 682 helix: 1.95 (1.63), residues: 12 sheet: 0.90 (0.32), residues: 277 loop : -0.45 (0.31), residues: 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 0.1803 time to fit residues: 17.5671 Evaluate side-chains 72 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0517 time to fit residues: 1.1598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.0040 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 5497 Z= 0.224 Angle : 0.679 10.740 7488 Z= 0.333 Chirality : 0.045 0.218 856 Planarity : 0.006 0.106 951 Dihedral : 8.507 139.044 784 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.33), residues: 682 helix: 1.98 (1.62), residues: 12 sheet: 0.66 (0.32), residues: 286 loop : -0.33 (0.32), residues: 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.1758 time to fit residues: 16.9040 Evaluate side-chains 70 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0532 time to fit residues: 1.0727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0070 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 1.1016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.157 5497 Z= 0.300 Angle : 0.746 17.212 7488 Z= 0.385 Chirality : 0.045 0.238 856 Planarity : 0.008 0.143 951 Dihedral : 8.545 139.630 784 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % 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: 0.20 (0.33), residues: 682 helix: 2.11 (1.63), residues: 12 sheet: 0.71 (0.32), residues: 285 loop : -0.34 (0.32), residues: 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1737 time to fit residues: 16.2195 Evaluate side-chains 68 residues out of total 601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 0.0030 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.105455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.090287 restraints weight = 19933.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.092543 restraints weight = 12456.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.094155 restraints weight = 8866.983| |-----------------------------------------------------------------------------| r_work (final): 0.4907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 5497 Z= 0.207 Angle : 0.689 11.783 7488 Z= 0.336 Chirality : 0.045 0.310 856 Planarity : 0.006 0.127 951 Dihedral : 8.513 139.966 784 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.33), residues: 682 helix: 2.15 (1.65), residues: 12 sheet: 0.90 (0.32), residues: 281 loop : -0.48 (0.32), residues: 389 =============================================================================== Job complete usr+sys time: 1404.42 seconds wall clock time: 30 minutes 13.98 seconds (1813.98 seconds total)