Starting phenix.real_space_refine (version: dev) on Sat Feb 18 01:37:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/02_2023/7r0c_14221_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/02_2023/7r0c_14221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/02_2023/7r0c_14221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/02_2023/7r0c_14221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/02_2023/7r0c_14221_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0c_14221/02_2023/7r0c_14221_updated.pdb" } resolution = 4.73 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= -0.001 sd= 0.035 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 Process input model Symmetric amino acids flipped Residue "A GLU 40": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2181 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "C" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2810 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1750 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 4.33, per 1000 atoms: 0.64 Number of scatterers: 6816 At special positions: 0 Unit cell: (83.2, 99.84, 139.52, 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 39 16.00 P 6 15.00 O 1248 8.00 N 1158 7.00 C 4365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 6 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 978.3 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 10 sheets defined 26.4% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 34 through 68 Processing helix chain 'A' and resid 73 through 102 removed outlier: 3.924A pdb=" N ILE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 110 through 141 removed outlier: 4.572A pdb=" N GLY A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 205 through 229 removed outlier: 5.019A pdb=" N ALA A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix removed outlier: 3.938A pdb=" N ILE A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.641A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 4.324A pdb=" N ASN A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.574A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing sheet with id= A, first strand: chain 'C' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'C' and resid 26 through 28 removed outlier: 7.216A pdb=" N ARG C 169 " --> pdb=" O PHE C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 163 through 168 removed outlier: 5.157A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N CYS C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL C 81 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'C' and resid 183 through 188 Processing sheet with id= F, first strand: chain 'C' and resid 343 through 349 removed outlier: 4.128A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 241 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN C 248 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 7 through 9 Processing sheet with id= H, first strand: chain 'D' and resid 88 through 93 removed outlier: 5.897A pdb=" N GLN D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU D 49 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 129 through 133 Processing sheet with id= J, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.395A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 783 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: 1.68 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1179 1.32 - 1.45: 1797 1.45 - 1.57: 3926 1.57 - 1.69: 22 1.69 - 1.81: 52 Bond restraints: 6976 Sorted by residual: bond pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.717 1.620 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O1P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O1P TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O3P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 6971 not shown) Histogram of bond angle deviations from ideal: 95.08 - 102.88: 37 102.88 - 110.68: 2246 110.68 - 118.48: 3249 118.48 - 126.28: 3847 126.28 - 134.08: 121 Bond angle restraints: 9500 Sorted by residual: angle pdb=" N ILE A 74 " pdb=" CA ILE A 74 " pdb=" C ILE A 74 " ideal model delta sigma weight residual 110.42 101.79 8.63 9.60e-01 1.09e+00 8.08e+01 angle pdb=" N VAL A 76 " pdb=" CA VAL A 76 " pdb=" C VAL A 76 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.93e+01 angle pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 113.84 107.29 6.55 1.30e+00 5.92e-01 2.53e+01 angle pdb=" CA LYS D 202 " pdb=" CB LYS D 202 " pdb=" CG LYS D 202 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C LEU C 68 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " ideal model delta sigma weight residual 122.61 129.40 -6.79 1.56e+00 4.11e-01 1.89e+01 ... (remaining 9495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 3812 16.88 - 33.77: 308 33.77 - 50.65: 54 50.65 - 67.54: 9 67.54 - 84.42: 8 Dihedral angle restraints: 4191 sinusoidal: 1628 harmonic: 2563 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -141.74 55.74 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS B 1 " pdb=" SG CYS B 1 " pdb=" SG CYS B 6 " pdb=" CB CYS B 6 " ideal model delta sinusoidal sigma weight residual 93.00 45.16 47.84 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA ARG D 226 " pdb=" C ARG D 226 " pdb=" N GLN D 227 " pdb=" CA GLN D 227 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 4188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1040 0.108 - 0.215: 43 0.215 - 0.323: 1 0.323 - 0.430: 1 0.430 - 0.538: 1 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.97 -0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CA TRP A 71 " pdb=" N TRP A 71 " pdb=" C TRP A 71 " pdb=" CB TRP A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1083 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.015 2.00e-02 2.50e+03 1.55e-02 6.01e+00 pdb=" CG TRP A 99 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 94 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 95 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 359 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO C 360 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 193 2.66 - 3.22: 7065 3.22 - 3.78: 11210 3.78 - 4.34: 14385 4.34 - 4.90: 22458 Nonbonded interactions: 55311 Sorted by model distance: nonbonded pdb=" O ASN C 222 " pdb=" N SER C 265 " model vdw 2.100 2.520 nonbonded pdb=" OE1 GLN D 9 " pdb=" OG1 THR D 105 " model vdw 2.127 2.440 nonbonded pdb=" O GLN D 40 " pdb=" N LYS D 48 " model vdw 2.178 2.520 nonbonded pdb=" OG1 THR C 56 " pdb=" O ALA C 82 " model vdw 2.190 2.440 nonbonded pdb=" NZ LYS C 11 " pdb=" O ARG C 165 " model vdw 2.207 2.520 ... (remaining 55306 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 39 5.16 5 C 4365 2.51 5 N 1158 2.21 5 O 1248 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 2.990 Check model and map are aligned: 0.100 Process input model: 21.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 0.110 6976 Z= 0.316 Angle : 0.909 12.782 9500 Z= 0.523 Chirality : 0.052 0.538 1086 Planarity : 0.005 0.060 1192 Dihedral : 13.187 84.422 2516 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 846 helix: -0.59 (0.32), residues: 209 sheet: -0.36 (0.34), residues: 245 loop : -0.59 (0.32), residues: 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2054 time to fit residues: 35.4779 Evaluate side-chains 91 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0654 time to fit residues: 1.2304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 0.0000 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN C 122 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 6976 Z= 0.168 Angle : 0.613 6.735 9500 Z= 0.310 Chirality : 0.044 0.162 1086 Planarity : 0.004 0.057 1192 Dihedral : 6.288 78.689 965 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.29), residues: 846 helix: 0.05 (0.34), residues: 206 sheet: -0.10 (0.34), residues: 246 loop : -0.56 (0.32), residues: 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1800 time to fit residues: 31.7824 Evaluate side-chains 90 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN C 122 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 6976 Z= 0.162 Angle : 0.597 6.385 9500 Z= 0.302 Chirality : 0.043 0.152 1086 Planarity : 0.004 0.057 1192 Dihedral : 6.121 77.686 965 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 846 helix: 0.22 (0.34), residues: 207 sheet: 0.11 (0.34), residues: 252 loop : -0.51 (0.32), residues: 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2037 time to fit residues: 35.0264 Evaluate side-chains 92 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 40 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 22 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 172 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6976 Z= 0.165 Angle : 0.600 7.214 9500 Z= 0.299 Chirality : 0.043 0.149 1086 Planarity : 0.004 0.056 1192 Dihedral : 6.072 77.687 965 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 846 helix: 0.37 (0.34), residues: 206 sheet: 0.15 (0.34), residues: 245 loop : -0.55 (0.32), residues: 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.2057 time to fit residues: 34.1007 Evaluate side-chains 90 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 159 HIS C 172 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6976 Z= 0.186 Angle : 0.606 6.644 9500 Z= 0.307 Chirality : 0.044 0.147 1086 Planarity : 0.004 0.056 1192 Dihedral : 6.107 78.306 965 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 846 helix: 0.25 (0.34), residues: 206 sheet: 0.03 (0.34), residues: 248 loop : -0.48 (0.32), residues: 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1920 time to fit residues: 30.5659 Evaluate side-chains 92 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6976 Z= 0.180 Angle : 0.614 6.744 9500 Z= 0.311 Chirality : 0.044 0.153 1086 Planarity : 0.005 0.060 1192 Dihedral : 6.115 78.217 965 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 846 helix: 0.33 (0.35), residues: 206 sheet: -0.11 (0.33), residues: 252 loop : -0.44 (0.33), residues: 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1963 time to fit residues: 31.1012 Evaluate side-chains 90 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 6976 Z= 0.261 Angle : 0.668 7.275 9500 Z= 0.344 Chirality : 0.044 0.148 1086 Planarity : 0.005 0.059 1192 Dihedral : 6.381 80.400 965 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 846 helix: 0.15 (0.35), residues: 206 sheet: -0.28 (0.33), residues: 252 loop : -0.35 (0.34), residues: 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2027 time to fit residues: 30.9082 Evaluate side-chains 90 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 40 optimal weight: 0.0370 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 6976 Z= 0.254 Angle : 0.687 7.199 9500 Z= 0.350 Chirality : 0.046 0.156 1086 Planarity : 0.005 0.058 1192 Dihedral : 6.527 80.104 965 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 27.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.29), residues: 846 helix: -0.06 (0.34), residues: 206 sheet: -0.50 (0.32), residues: 248 loop : -0.47 (0.34), residues: 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.2058 time to fit residues: 31.4991 Evaluate side-chains 87 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6976 Z= 0.186 Angle : 0.668 7.939 9500 Z= 0.337 Chirality : 0.045 0.181 1086 Planarity : 0.006 0.092 1192 Dihedral : 6.300 78.571 965 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.29), residues: 846 helix: -0.00 (0.34), residues: 209 sheet: -0.25 (0.33), residues: 243 loop : -0.53 (0.34), residues: 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1882 time to fit residues: 30.4076 Evaluate side-chains 90 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.0370 chunk 56 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6976 Z= 0.165 Angle : 0.674 7.868 9500 Z= 0.337 Chirality : 0.046 0.240 1086 Planarity : 0.006 0.124 1192 Dihedral : 6.165 76.555 965 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.29), residues: 846 helix: 0.04 (0.35), residues: 209 sheet: -0.25 (0.33), residues: 256 loop : -0.62 (0.33), residues: 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2178 time to fit residues: 34.7408 Evaluate side-chains 93 residues out of total 742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.112538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091132 restraints weight = 28345.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.094093 restraints weight = 17904.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.096097 restraints weight = 12865.893| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6976 Z= 0.179 Angle : 0.660 7.631 9500 Z= 0.328 Chirality : 0.045 0.200 1086 Planarity : 0.006 0.123 1192 Dihedral : 6.108 77.092 965 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 846 helix: 0.12 (0.35), residues: 209 sheet: -0.31 (0.33), residues: 252 loop : -0.49 (0.33), residues: 385 =============================================================================== Job complete usr+sys time: 1605.46 seconds wall clock time: 30 minutes 18.89 seconds (1818.89 seconds total)