Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 21:29:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/07_2023/7r0j_14223_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/07_2023/7r0j_14223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/07_2023/7r0j_14223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/07_2023/7r0j_14223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/07_2023/7r0j_14223_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0j_14223/07_2023/7r0j_14223_updated.pdb" } resolution = 4.23 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= 0.019 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 19 5.16 5 C 2947 2.51 5 N 793 2.21 5 O 904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 118": "OE1" <-> "OE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 4669 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2815 Classifications: {'peptide': 354} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 325} 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: 2.81, per 1000 atoms: 0.60 Number of scatterers: 4669 At special positions: 0 Unit cell: (87.04, 99.84, 88.32, 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 19 16.00 P 6 15.00 O 904 8.00 N 793 7.00 C 2947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 700.9 milliseconds 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 5 helices and 12 sheets defined 3.7% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' 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: 7.526A 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 76 through 78 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: 3.811A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 53 through 59 removed outlier: 6.254A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL C 81 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 7 through 9 Processing sheet with id= I, first strand: chain 'D' and resid 13 through 15 removed outlier: 5.567A pdb=" N LYS D 106 " --> pdb=" O LEU D 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 88 through 93 removed outlier: 5.764A pdb=" N GLN D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 49 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 129 through 133 Processing sheet with id= L, first strand: chain 'D' and resid 136 through 138 removed outlier: 5.925A pdb=" N ARG D 164 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TRP D 173 " --> pdb=" O ARG D 164 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 384 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: 1.26 Time building geometry restraints manager: 2.22 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: 1499 1.34 - 1.46: 1124 1.46 - 1.58: 2103 1.58 - 1.70: 22 1.70 - 1.82: 24 Bond restraints: 4772 Sorted by residual: bond pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" OG1 TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.717 1.616 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C ASN C 122 " pdb=" N LEU C 123 " ideal model delta sigma weight residual 1.331 1.257 0.075 1.59e-02 3.96e+03 2.21e+01 bond pdb=" O1P TPO A 359 " pdb=" P TPO A 359 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O1P TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 1.525 1.608 -0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 4767 not shown) Histogram of bond angle deviations from ideal: 94.97 - 102.81: 19 102.81 - 110.64: 1630 110.64 - 118.48: 2132 118.48 - 126.32: 2643 126.32 - 134.15: 62 Bond angle restraints: 6486 Sorted by residual: angle pdb=" C GLN D 41 " pdb=" N LYS D 42 " pdb=" CA LYS D 42 " ideal model delta sigma weight residual 121.80 134.13 -12.33 2.44e+00 1.68e-01 2.55e+01 angle pdb=" CB TPO A 360 " pdb=" OG1 TPO A 360 " pdb=" P TPO A 360 " ideal model delta sigma weight residual 119.31 105.14 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N GLY C 141 " pdb=" CA GLY C 141 " pdb=" C GLY C 141 " ideal model delta sigma weight residual 110.74 117.04 -6.30 1.37e+00 5.33e-01 2.11e+01 angle pdb=" N LYS C 49 " pdb=" CA LYS C 49 " pdb=" C LYS C 49 " ideal model delta sigma weight residual 114.31 108.80 5.51 1.29e+00 6.01e-01 1.82e+01 angle pdb=" N ASP C 259 " pdb=" CA ASP C 259 " pdb=" C ASP C 259 " ideal model delta sigma weight residual 112.97 109.15 3.82 1.06e+00 8.90e-01 1.30e+01 ... (remaining 6481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2650 17.88 - 35.77: 205 35.77 - 53.65: 30 53.65 - 71.53: 5 71.53 - 89.41: 6 Dihedral angle restraints: 2896 sinusoidal: 1152 harmonic: 1744 Sorted by residual: dihedral pdb=" CB CYS D 26 " pdb=" SG CYS D 26 " pdb=" SG CYS D 91 " pdb=" CB CYS D 91 " ideal model delta sinusoidal sigma weight residual 93.00 49.57 43.43 1 1.00e+01 1.00e-02 2.63e+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 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS C 17 " pdb=" C LYS C 17 " pdb=" N LEU C 18 " pdb=" CA LEU C 18 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 2893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 433 0.035 - 0.069: 180 0.069 - 0.103: 86 0.103 - 0.138: 23 0.138 - 0.172: 5 Chirality restraints: 727 Sorted by residual: chirality pdb=" CG LEU D 76 " pdb=" CB LEU D 76 " pdb=" CD1 LEU D 76 " pdb=" CD2 LEU D 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA VAL C 81 " pdb=" N VAL C 81 " pdb=" C VAL C 81 " pdb=" CB VAL C 81 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA VAL C 220 " pdb=" N VAL C 220 " pdb=" C VAL C 220 " pdb=" CB VAL C 220 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 724 not shown) Planarity restraints: 825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 236 " -0.011 2.00e-02 2.50e+03 1.62e-02 6.56e+00 pdb=" CG TRP D 236 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP D 236 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 236 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 236 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 236 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 236 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 236 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 236 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 236 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 229 " 0.010 2.00e-02 2.50e+03 1.39e-02 4.86e+00 pdb=" CG TRP D 229 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP D 229 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 229 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 229 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 229 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 229 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 229 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 229 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 195 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 196 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " -0.026 5.00e-02 4.00e+02 ... (remaining 822 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 126 2.60 - 3.18: 4602 3.18 - 3.75: 7652 3.75 - 4.33: 10290 4.33 - 4.90: 15830 Nonbonded interactions: 38500 Sorted by model distance: nonbonded pdb=" O ASP D 85 " pdb=" OH TYR D 89 " model vdw 2.029 2.440 nonbonded pdb=" NE2 GLN D 92 " pdb=" O GLN D 93 " model vdw 2.186 2.520 nonbonded pdb=" N GLN C 130 " pdb=" O LEU C 287 " model vdw 2.188 2.520 nonbonded pdb=" O ALA C 263 " pdb=" OG SER C 266 " model vdw 2.191 2.440 nonbonded pdb=" O SER D 178 " pdb=" N GLY D 182 " model vdw 2.193 2.520 ... (remaining 38495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.090 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: 1.070 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.008 0.115 4772 Z= 0.495 Angle : 1.034 14.169 6486 Z= 0.554 Chirality : 0.048 0.172 727 Planarity : 0.006 0.055 825 Dihedral : 13.438 89.415 1765 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 37.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.99 (0.35), residues: 577 helix: -1.30 (1.09), residues: 17 sheet: -0.35 (0.34), residues: 245 loop : -0.80 (0.36), residues: 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1678 time to fit residues: 23.2922 Evaluate side-chains 82 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4772 Z= 0.184 Angle : 0.635 7.436 6486 Z= 0.318 Chirality : 0.043 0.138 727 Planarity : 0.004 0.041 825 Dihedral : 7.964 83.946 667 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.64 (0.36), residues: 577 helix: -0.62 (1.29), residues: 17 sheet: 0.05 (0.34), residues: 242 loop : -0.75 (0.36), residues: 318 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1573 time to fit residues: 22.8452 Evaluate side-chains 81 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 4772 Z= 0.356 Angle : 0.735 8.411 6486 Z= 0.375 Chirality : 0.043 0.131 727 Planarity : 0.005 0.044 825 Dihedral : 8.125 80.958 667 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 33.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.01 (0.34), residues: 577 helix: -1.01 (1.19), residues: 17 sheet: -0.52 (0.32), residues: 246 loop : -0.68 (0.36), residues: 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1554 time to fit residues: 20.4933 Evaluate side-chains 77 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 4772 Z= 0.375 Angle : 0.742 8.611 6486 Z= 0.377 Chirality : 0.044 0.220 727 Planarity : 0.005 0.047 825 Dihedral : 8.238 81.115 667 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 32.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.30 (0.34), residues: 577 helix: -1.37 (1.09), residues: 17 sheet: -0.81 (0.32), residues: 245 loop : -0.79 (0.36), residues: 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1546 time to fit residues: 20.1201 Evaluate side-chains 71 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 HIS C 198 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 4772 Z= 0.386 Angle : 0.760 8.652 6486 Z= 0.388 Chirality : 0.045 0.219 727 Planarity : 0.005 0.040 825 Dihedral : 8.363 81.066 667 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 34.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.51 (0.34), residues: 577 helix: -1.54 (1.01), residues: 17 sheet: -1.00 (0.32), residues: 244 loop : -0.88 (0.36), residues: 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1603 time to fit residues: 20.8917 Evaluate side-chains 71 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 4772 Z= 0.341 Angle : 0.742 8.210 6486 Z= 0.377 Chirality : 0.045 0.205 727 Planarity : 0.005 0.043 825 Dihedral : 8.361 81.529 667 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 33.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.35), residues: 577 helix: -1.55 (1.13), residues: 17 sheet: -1.09 (0.31), residues: 250 loop : -0.83 (0.36), residues: 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1684 time to fit residues: 19.6458 Evaluate side-chains 70 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 4772 Z= 0.307 Angle : 0.710 7.894 6486 Z= 0.361 Chirality : 0.044 0.188 727 Planarity : 0.005 0.041 825 Dihedral : 8.280 82.416 667 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 31.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.34), residues: 577 helix: -1.90 (1.00), residues: 23 sheet: -0.98 (0.31), residues: 239 loop : -0.90 (0.36), residues: 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1722 time to fit residues: 20.6410 Evaluate side-chains 73 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4772 Z= 0.191 Angle : 0.655 8.923 6486 Z= 0.325 Chirality : 0.044 0.182 727 Planarity : 0.004 0.042 825 Dihedral : 7.972 83.013 667 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.25 (0.34), residues: 577 helix: -1.37 (1.13), residues: 17 sheet: -0.58 (0.32), residues: 230 loop : -0.94 (0.35), residues: 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1608 time to fit residues: 21.0458 Evaluate side-chains 77 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 4772 Z= 0.264 Angle : 0.708 8.419 6486 Z= 0.353 Chirality : 0.044 0.154 727 Planarity : 0.005 0.044 825 Dihedral : 8.050 82.007 667 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.34), residues: 577 helix: -1.75 (0.96), residues: 23 sheet: -0.61 (0.33), residues: 214 loop : -0.95 (0.34), residues: 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.516 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: 95 average time/residue: 0.1584 time to fit residues: 19.4828 Evaluate side-chains 77 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 36 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN D 238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4772 Z= 0.336 Angle : 0.749 7.790 6486 Z= 0.381 Chirality : 0.046 0.147 727 Planarity : 0.005 0.044 825 Dihedral : 8.288 83.211 667 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 31.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.38 (0.34), residues: 577 helix: -1.73 (1.02), residues: 23 sheet: -0.70 (0.33), residues: 215 loop : -0.95 (0.35), residues: 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.585 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: 98 average time/residue: 0.1619 time to fit residues: 20.5248 Evaluate side-chains 72 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 198 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060967 restraints weight = 20126.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063289 restraints weight = 12480.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064893 restraints weight = 8893.443| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 4772 Z= 0.311 Angle : 0.728 8.786 6486 Z= 0.369 Chirality : 0.045 0.146 727 Planarity : 0.005 0.046 825 Dihedral : 8.279 83.082 667 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 31.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.31 (0.35), residues: 577 helix: -1.49 (1.17), residues: 17 sheet: -0.64 (0.34), residues: 216 loop : -0.96 (0.34), residues: 344 =============================================================================== Job complete usr+sys time: 1137.44 seconds wall clock time: 21 minutes 34.74 seconds (1294.74 seconds total)