Starting phenix.real_space_refine on Thu Nov 14 15:22:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iow_35627/11_2024/8iow_35627.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iow_35627/11_2024/8iow_35627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iow_35627/11_2024/8iow_35627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iow_35627/11_2024/8iow_35627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iow_35627/11_2024/8iow_35627.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iow_35627/11_2024/8iow_35627.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3017 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2628 2.51 5 N 721 2.21 5 O 811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4178 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 863 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "D2" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 107 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "H" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1561 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.12, per 1000 atoms: 0.99 Number of scatterers: 4178 At special positions: 0 Unit cell: (58.22, 67.24, 104.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 811 8.00 N 721 7.00 C 2628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYSD2 121 " - pdb=" SG CYSD2 132 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG I 401 " - " ASN I 221 " " NAG I 402 " - " ASN I 245 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 503.3 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 6.7% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.300A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.945A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 4.049A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.686A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 192 Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing sheet with id=AA1, first strand: chain 'I' and resid 223 through 225 Processing sheet with id=AA2, first strand: chain 'I' and resid 266 through 269 removed outlier: 3.856A pdb=" N THR I 266 " --> pdb=" O TYR I 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.959A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.423A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.604A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.426A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.720A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY H 50 " --> pdb=" O GLY H 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 73 Processing sheet with id=AB4, first strand: chain 'H' and resid 123 through 127 removed outlier: 5.034A pdb=" N ALA H 140 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL H 187 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY H 142 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL H 185 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU H 144 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER H 183 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS H 146 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU H 181 " --> pdb=" O LYS H 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 123 through 127 removed outlier: 5.034A pdb=" N ALA H 140 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL H 187 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY H 142 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL H 185 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU H 144 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER H 183 " --> pdb=" O LEU H 144 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS H 146 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU H 181 " --> pdb=" O LYS H 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 157 removed outlier: 3.547A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR H 197 " --> pdb=" O VAL H 214 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 300 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: 1.11 Time building geometry restraints manager: 1.12 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: 1330 1.34 - 1.46: 973 1.46 - 1.58: 1954 1.58 - 1.69: 1 1.69 - 1.81: 24 Bond restraints: 4282 Sorted by residual: bond pdb=" C1 NAG I 402 " pdb=" O5 NAG I 402 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" CA VAL I 227 " pdb=" CB VAL I 227 " ideal model delta sigma weight residual 1.530 1.555 -0.025 1.11e-02 8.12e+03 4.99e+00 bond pdb=" CB PRO I 308 " pdb=" CG PRO I 308 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.69e+00 bond pdb=" C1 NAG I 401 " pdb=" O5 NAG I 401 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" SD MET I 269 " pdb=" CE MET I 269 " ideal model delta sigma weight residual 1.791 1.750 0.041 2.50e-02 1.60e+03 2.64e+00 ... (remaining 4277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5557 2.04 - 4.07: 208 4.07 - 6.11: 33 6.11 - 8.15: 17 8.15 - 10.19: 3 Bond angle restraints: 5818 Sorted by residual: angle pdb=" CA PRO I 308 " pdb=" N PRO I 308 " pdb=" CD PRO I 308 " ideal model delta sigma weight residual 112.00 105.65 6.35 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 112.96 109.10 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C GLY L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" CG ARG H 26 " pdb=" CD ARG H 26 " pdb=" NE ARG H 26 " ideal model delta sigma weight residual 112.00 119.57 -7.57 2.20e+00 2.07e-01 1.18e+01 angle pdb=" CA TYR I 257 " pdb=" CB TYR I 257 " pdb=" CG TYR I 257 " ideal model delta sigma weight residual 113.90 120.07 -6.17 1.80e+00 3.09e-01 1.17e+01 ... (remaining 5813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 2253 16.03 - 32.05: 238 32.05 - 48.08: 59 48.08 - 64.10: 16 64.10 - 80.13: 5 Dihedral angle restraints: 2571 sinusoidal: 1027 harmonic: 1544 Sorted by residual: dihedral pdb=" CA VAL H 114 " pdb=" C VAL H 114 " pdb=" N SER H 115 " pdb=" CA SER H 115 " ideal model delta harmonic sigma weight residual -180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CB CYS H 143 " pdb=" SG CYS H 143 " pdb=" SG CYS H 199 " pdb=" CB CYS H 199 " ideal model delta sinusoidal sigma weight residual -86.00 -39.25 -46.75 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" CB CYSD2 121 " pdb=" SG CYSD2 121 " pdb=" SG CYSD2 132 " pdb=" CB CYSD2 132 " ideal model delta sinusoidal sigma weight residual -86.00 -131.40 45.40 1 1.00e+01 1.00e-02 2.86e+01 ... (remaining 2568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 536 0.075 - 0.151: 95 0.151 - 0.226: 4 0.226 - 0.301: 4 0.301 - 0.376: 2 Chirality restraints: 641 Sorted by residual: chirality pdb=" C1 NAG I 402 " pdb=" ND2 ASN I 245 " pdb=" C2 NAG I 402 " pdb=" O5 NAG I 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB THR I 266 " pdb=" CA THR I 266 " pdb=" OG1 THR I 266 " pdb=" CG2 THR I 266 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE I 213 " pdb=" CA ILE I 213 " pdb=" CG1 ILE I 213 " pdb=" CG2 ILE I 213 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 638 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 307 " 0.090 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO I 308 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO I 308 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO I 308 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 53 " -0.034 2.00e-02 2.50e+03 2.88e-02 2.08e+01 pdb=" CG TRP H 53 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP H 53 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP H 53 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 53 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 53 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 53 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 53 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP H 53 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO L 95 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.042 5.00e-02 4.00e+02 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1061 2.80 - 3.32: 3522 3.32 - 3.85: 7158 3.85 - 4.37: 8163 4.37 - 4.90: 14551 Nonbonded interactions: 34455 Sorted by model distance: nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP L 170 " pdb=" OG1 THR L 172 " model vdw 2.291 3.040 nonbonded pdb=" NH1 ARG L 61 " pdb=" OD2 ASP L 82 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASN H 202 " pdb=" NZ LYS H 204 " model vdw 2.330 3.120 nonbonded pdb=" O SERD2 128 " pdb=" OG SERD2 128 " model vdw 2.335 3.040 ... (remaining 34450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.007 0.096 4282 Z= 0.421 Angle : 0.984 10.186 5818 Z= 0.530 Chirality : 0.061 0.376 641 Planarity : 0.009 0.132 745 Dihedral : 14.462 80.127 1562 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.35), residues: 527 helix: -2.63 (1.00), residues: 14 sheet: -1.33 (0.34), residues: 218 loop : -1.61 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP H 53 HIS 0.005 0.001 HIS I 288 PHE 0.036 0.004 PHE L 94 TYR 0.033 0.003 TYR L 173 ARG 0.016 0.002 ARG I 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.455 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2622 time to fit residues: 23.0050 Evaluate side-chains 65 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 242 HIS L 90 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4282 Z= 0.263 Angle : 0.656 8.033 5818 Z= 0.345 Chirality : 0.047 0.285 641 Planarity : 0.006 0.070 745 Dihedral : 6.791 46.008 617 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.52 % Allowed : 8.46 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.37), residues: 527 helix: -1.86 (1.15), residues: 14 sheet: -1.11 (0.34), residues: 224 loop : -1.09 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 53 HIS 0.007 0.001 HIS L 189 PHE 0.029 0.002 PHE H 149 TYR 0.011 0.002 TYR L 173 ARG 0.006 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: I 287 ARG cc_start: 0.5760 (tpm170) cc_final: 0.5511 (tpm170) REVERT: L 208 SER cc_start: 0.8054 (m) cc_final: 0.7791 (p) REVERT: H 180 SER cc_start: 0.8096 (t) cc_final: 0.7818 (p) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.2306 time to fit residues: 23.5737 Evaluate side-chains 77 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain H residue 30 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 42 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4282 Z= 0.254 Angle : 0.623 7.431 5818 Z= 0.325 Chirality : 0.046 0.272 641 Planarity : 0.005 0.067 745 Dihedral : 5.962 35.317 617 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.52 % Allowed : 11.71 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.37), residues: 527 helix: -1.72 (1.11), residues: 14 sheet: -1.03 (0.33), residues: 231 loop : -0.99 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.005 0.001 HIS L 189 PHE 0.026 0.002 PHE H 149 TYR 0.013 0.001 TYR L 173 ARG 0.007 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: I 276 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6632 (p90) REVERT: L 79 GLN cc_start: 0.8141 (mm110) cc_final: 0.7939 (mm110) REVERT: L 208 SER cc_start: 0.7936 (m) cc_final: 0.7664 (p) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 0.2369 time to fit residues: 23.5842 Evaluate side-chains 78 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.0050 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4282 Z= 0.325 Angle : 0.649 7.859 5818 Z= 0.336 Chirality : 0.046 0.273 641 Planarity : 0.005 0.065 745 Dihedral : 6.033 35.495 617 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.25 % Allowed : 13.67 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.37), residues: 527 helix: -1.67 (1.14), residues: 14 sheet: -1.02 (0.33), residues: 231 loop : -1.00 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 106 HIS 0.006 0.001 HIS L 189 PHE 0.028 0.002 PHE H 149 TYR 0.014 0.002 TYR L 173 ARG 0.005 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: I 276 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6673 (p90) REVERT: L 208 SER cc_start: 0.7948 (m) cc_final: 0.7688 (p) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.2660 time to fit residues: 27.7970 Evaluate side-chains 84 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 239 GLN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4282 Z= 0.261 Angle : 0.614 7.271 5818 Z= 0.317 Chirality : 0.045 0.260 641 Planarity : 0.005 0.063 745 Dihedral : 5.876 34.857 617 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.60 % Allowed : 15.62 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.37), residues: 527 helix: -1.22 (1.25), residues: 14 sheet: -0.92 (0.33), residues: 228 loop : -1.02 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 233 HIS 0.005 0.001 HIS L 189 PHE 0.025 0.002 PHE H 149 TYR 0.012 0.001 TYR L 173 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7112 (mm) REVERT: I 276 HIS cc_start: 0.7031 (OUTLIER) cc_final: 0.6692 (p90) REVERT: L 90 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8709 (tm130) outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 0.2241 time to fit residues: 22.4692 Evaluate side-chains 85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 156 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4282 Z= 0.230 Angle : 0.597 7.045 5818 Z= 0.309 Chirality : 0.045 0.251 641 Planarity : 0.005 0.063 745 Dihedral : 5.787 33.858 617 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.04 % Allowed : 16.27 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.37), residues: 527 helix: -1.19 (1.26), residues: 14 sheet: -0.82 (0.33), residues: 227 loop : -1.01 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.004 0.001 HIS L 189 PHE 0.024 0.002 PHE H 149 TYR 0.015 0.001 TYR L 173 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7122 (mm) REVERT: I 276 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6663 (p90) REVERT: H 53 TRP cc_start: 0.8733 (OUTLIER) cc_final: 0.8392 (p90) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.2615 time to fit residues: 28.2567 Evaluate side-chains 86 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 275 HIS L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4282 Z= 0.278 Angle : 0.620 7.516 5818 Z= 0.321 Chirality : 0.046 0.245 641 Planarity : 0.005 0.063 745 Dihedral : 5.824 34.858 617 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.47 % Allowed : 17.79 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.37), residues: 527 helix: -1.25 (1.25), residues: 14 sheet: -0.82 (0.33), residues: 230 loop : -1.13 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 233 HIS 0.004 0.001 HIS L 189 PHE 0.026 0.002 PHE H 149 TYR 0.014 0.002 TYR L 173 ARG 0.005 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7140 (mm) REVERT: I 276 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.6728 (p90) REVERT: H 53 TRP cc_start: 0.8771 (OUTLIER) cc_final: 0.8400 (p90) outliers start: 16 outliers final: 8 residues processed: 88 average time/residue: 0.2540 time to fit residues: 26.6685 Evaluate side-chains 86 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4282 Z= 0.277 Angle : 0.621 7.508 5818 Z= 0.321 Chirality : 0.046 0.242 641 Planarity : 0.005 0.062 745 Dihedral : 5.843 35.614 617 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.69 % Allowed : 17.79 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.37), residues: 527 helix: -1.20 (1.28), residues: 14 sheet: -0.82 (0.33), residues: 230 loop : -1.06 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 233 HIS 0.003 0.001 HIS L 189 PHE 0.025 0.002 PHE H 149 TYR 0.013 0.002 TYR L 173 ARG 0.006 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7125 (mm) REVERT: I 276 HIS cc_start: 0.7141 (OUTLIER) cc_final: 0.6767 (p90) REVERT: H 53 TRP cc_start: 0.8796 (OUTLIER) cc_final: 0.8433 (p90) REVERT: H 83 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6906 (mtt) outliers start: 17 outliers final: 10 residues processed: 88 average time/residue: 0.2368 time to fit residues: 24.7835 Evaluate side-chains 90 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4282 Z= 0.259 Angle : 0.619 7.344 5818 Z= 0.319 Chirality : 0.045 0.233 641 Planarity : 0.005 0.062 745 Dihedral : 5.813 35.501 617 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.04 % Allowed : 18.87 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.37), residues: 527 helix: -1.18 (1.28), residues: 14 sheet: -0.73 (0.34), residues: 224 loop : -1.11 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 233 HIS 0.002 0.001 HIS H 203 PHE 0.025 0.002 PHE H 149 TYR 0.015 0.002 TYR L 173 ARG 0.006 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7103 (mm) REVERT: H 53 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.8368 (p90) REVERT: H 83 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.6857 (mtt) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.2330 time to fit residues: 23.4355 Evaluate side-chains 89 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 4282 Z= 0.486 Angle : 0.751 8.844 5818 Z= 0.388 Chirality : 0.050 0.256 641 Planarity : 0.006 0.066 745 Dihedral : 6.349 43.301 617 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.82 % Allowed : 19.09 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.36), residues: 527 helix: -1.56 (1.19), residues: 14 sheet: -0.93 (0.35), residues: 209 loop : -1.27 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 233 HIS 0.005 0.001 HIS I 242 PHE 0.031 0.003 PHE H 149 TYR 0.019 0.002 TYR L 173 ARG 0.007 0.001 ARG H 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: I 222 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7089 (mm) REVERT: I 276 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6779 (p90) REVERT: H 53 TRP cc_start: 0.8860 (OUTLIER) cc_final: 0.8473 (p90) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.2360 time to fit residues: 24.2668 Evaluate side-chains 85 residues out of total 461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 276 HIS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 53 TRP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 180 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 chunk 35 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.0570 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133369 restraints weight = 4853.051| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.94 r_work: 0.3477 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4282 Z= 0.203 Angle : 0.614 7.991 5818 Z= 0.315 Chirality : 0.045 0.219 641 Planarity : 0.005 0.060 745 Dihedral : 5.806 34.388 617 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.17 % Allowed : 20.82 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.37), residues: 527 helix: -0.94 (1.34), residues: 14 sheet: -0.80 (0.34), residues: 227 loop : -1.06 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 233 HIS 0.002 0.001 HIS I 242 PHE 0.021 0.002 PHE H 149 TYR 0.013 0.001 TYR L 173 ARG 0.007 0.001 ARG H 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.11 seconds wall clock time: 34 minutes 46.82 seconds (2086.82 seconds total)