Starting phenix.real_space_refine on Thu Nov 14 07:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/11_2024/8bf8_16016.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/11_2024/8bf8_16016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/11_2024/8bf8_16016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/11_2024/8bf8_16016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/11_2024/8bf8_16016.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/11_2024/8bf8_16016.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 111 5.49 5 S 1 5.16 5 C 2525 2.51 5 N 871 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2303 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2383 Classifications: {'RNA': 111} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 43} Link IDs: {'rna2p': 16, 'rna3p': 94} Chain breaks: 2 Time building chain proxies: 3.89, per 1000 atoms: 0.83 Number of scatterers: 4686 At special positions: 0 Unit cell: (84.032, 87.36, 84.864, 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 1 16.00 P 111 15.00 O 1178 8.00 N 871 7.00 C 2525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 333.7 milliseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 566 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 53.6% alpha, 16.2% beta 42 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 14 through 43 removed outlier: 3.645A pdb=" N ILE A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 75 through 94 removed outlier: 3.766A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 236 through 272 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.057A pdb=" N LYS A 153 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 172 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 157 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 159 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 161 " --> pdb=" O HIS A 166 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS A 166 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 171 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 201 153 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 872 1.33 - 1.45: 1746 1.45 - 1.57: 2169 1.57 - 1.68: 219 1.68 - 1.80: 1 Bond restraints: 5007 Sorted by residual: bond pdb=" O3' C B -63 " pdb=" P C B -62 " ideal model delta sigma weight residual 1.607 1.587 0.020 1.50e-02 4.44e+03 1.82e+00 bond pdb=" C GLY A 189 " pdb=" O GLY A 189 " ideal model delta sigma weight residual 1.243 1.233 0.010 9.30e-03 1.16e+04 1.15e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.25e-01 bond pdb=" CA ILE A 177 " pdb=" CB ILE A 177 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.55e-02 4.16e+03 8.01e-01 bond pdb=" CB PRO A 178 " pdb=" CG PRO A 178 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.39e-01 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 7116 1.20 - 2.40: 153 2.40 - 3.60: 34 3.60 - 4.80: 7 4.80 - 5.99: 2 Bond angle restraints: 7312 Sorted by residual: angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 119.89 -5.99 1.80e+00 3.09e-01 1.11e+01 angle pdb=" O4' A B -88 " pdb=" C1' A B -88 " pdb=" N9 A B -88 " ideal model delta sigma weight residual 108.20 112.12 -3.92 1.50e+00 4.44e-01 6.83e+00 angle pdb=" C2' G B -78 " pdb=" C1' G B -78 " pdb=" N9 G B -78 " ideal model delta sigma weight residual 112.00 114.91 -2.91 1.50e+00 4.44e-01 3.75e+00 angle pdb=" C THR A 123 " pdb=" N ASN A 124 " pdb=" CA ASN A 124 " ideal model delta sigma weight residual 122.46 124.93 -2.47 1.41e+00 5.03e-01 3.07e+00 angle pdb=" C2' A B -88 " pdb=" C1' A B -88 " pdb=" N9 A B -88 " ideal model delta sigma weight residual 114.00 116.60 -2.60 1.50e+00 4.44e-01 3.00e+00 ... (remaining 7307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2593 17.34 - 34.68: 225 34.68 - 52.02: 138 52.02 - 69.36: 155 69.36 - 86.70: 29 Dihedral angle restraints: 3140 sinusoidal: 2265 harmonic: 875 Sorted by residual: dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -84.08 -75.92 1 1.50e+01 4.44e-03 3.23e+01 dihedral pdb=" CB LYS A 233 " pdb=" CG LYS A 233 " pdb=" CD LYS A 233 " pdb=" CE LYS A 233 " ideal model delta sinusoidal sigma weight residual 60.00 117.41 -57.41 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" O5' C B -67 " pdb=" C5' C B -67 " pdb=" C4' C B -67 " pdb=" C3' C B -67 " ideal model delta sinusoidal sigma weight residual 55.00 -1.26 56.26 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 796 0.043 - 0.086: 89 0.086 - 0.129: 26 0.129 - 0.171: 0 0.171 - 0.214: 1 Chirality restraints: 912 Sorted by residual: chirality pdb=" C1' A B -88 " pdb=" O4' A B -88 " pdb=" C2' A B -88 " pdb=" N9 A B -88 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR A 309 " pdb=" N TYR A 309 " pdb=" C TYR A 309 " pdb=" CB TYR A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 275 " pdb=" N ILE A 275 " pdb=" C ILE A 275 " pdb=" CB ILE A 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 909 not shown) Planarity restraints: 514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B -88 " -0.028 2.00e-02 2.50e+03 1.38e-02 5.27e+00 pdb=" N9 A B -88 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A B -88 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B -88 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B -88 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B -88 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B -88 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B -88 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B -88 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B -88 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B -88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -78 " 0.026 2.00e-02 2.50e+03 1.08e-02 3.47e+00 pdb=" N9 G B -78 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B -78 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B -78 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B -78 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B -78 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B -78 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G B -78 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B -78 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B -78 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B -78 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B -78 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 309 " -0.015 2.00e-02 2.50e+03 1.18e-02 2.76e+00 pdb=" CG TYR A 309 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 309 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 309 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 309 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 309 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 309 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 309 " -0.000 2.00e-02 2.50e+03 ... (remaining 511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 4367 3.28 - 3.82: 9269 3.82 - 4.36: 10882 4.36 - 4.90: 15807 Nonbonded interactions: 40841 Sorted by model distance: nonbonded pdb=" O LEU A 261 " pdb=" OG1 THR A 265 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG A 238 " pdb=" O6 G B -33 " model vdw 2.243 3.120 nonbonded pdb=" O2' A B -66 " pdb=" O2 C B -63 " model vdw 2.252 3.040 nonbonded pdb=" O2 C B-107 " pdb=" N2 G B -6 " model vdw 2.284 3.120 nonbonded pdb=" O LYS A 263 " pdb=" OG SER A 267 " model vdw 2.307 3.040 ... (remaining 40836 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: 0.880 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.330 Find NCS groups from input model: 0.040 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.003 0.043 5007 Z= 0.178 Angle : 0.474 5.995 7312 Z= 0.248 Chirality : 0.031 0.214 912 Planarity : 0.003 0.022 514 Dihedral : 21.432 86.703 2574 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.93 % Allowed : 6.98 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.51), residues: 292 helix: 2.03 (0.40), residues: 151 sheet: -1.01 (0.85), residues: 44 loop : -0.84 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.005 0.002 HIS A 262 PHE 0.009 0.001 PHE A 35 TYR 0.029 0.002 TYR A 309 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.334 Fit side-chains REVERT: A 168 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 214 TYR cc_start: 0.8208 (m-80) cc_final: 0.7977 (m-80) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 1.3141 time to fit residues: 47.9048 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 64 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 147 GLN A 156 ASN A 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5007 Z= 0.247 Angle : 0.542 6.419 7312 Z= 0.279 Chirality : 0.035 0.201 912 Planarity : 0.004 0.021 514 Dihedral : 22.249 86.633 2071 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.86 % Allowed : 13.49 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.50), residues: 292 helix: 2.00 (0.40), residues: 152 sheet: -2.34 (1.40), residues: 16 loop : -0.90 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.010 0.001 PHE A 35 TYR 0.030 0.002 TYR A 309 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.334 Fit side-chains REVERT: A 147 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.6860 (tm130) REVERT: A 168 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 174 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6450 (mt-10) REVERT: A 214 TYR cc_start: 0.8219 (m-80) cc_final: 0.7924 (m-80) REVERT: A 223 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6074 (mmp-170) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 1.1855 time to fit residues: 38.4149 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5007 Z= 0.270 Angle : 0.549 6.608 7312 Z= 0.283 Chirality : 0.035 0.197 912 Planarity : 0.004 0.022 514 Dihedral : 22.199 84.677 2070 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.72 % Allowed : 13.95 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.49), residues: 292 helix: 1.89 (0.40), residues: 152 sheet: -1.51 (1.05), residues: 24 loop : -1.31 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 70 HIS 0.004 0.002 HIS A 262 PHE 0.007 0.001 PHE A 197 TYR 0.030 0.002 TYR A 309 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.393 Fit side-chains REVERT: A 147 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.6695 (tm130) REVERT: A 168 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 223 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6112 (mmp-170) REVERT: A 309 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7521 (p90) outliers start: 8 outliers final: 3 residues processed: 33 average time/residue: 1.1863 time to fit residues: 41.0620 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5007 Z= 0.305 Angle : 0.577 7.071 7312 Z= 0.296 Chirality : 0.036 0.196 912 Planarity : 0.004 0.025 514 Dihedral : 22.194 84.391 2070 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.19 % Allowed : 13.95 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.49), residues: 292 helix: 1.78 (0.39), residues: 152 sheet: -1.56 (1.03), residues: 24 loop : -1.40 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 PHE 0.007 0.001 PHE A 197 TYR 0.032 0.002 TYR A 309 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.331 Fit side-chains REVERT: A 147 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7158 (tm130) REVERT: A 168 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7639 (mt-10) REVERT: A 223 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6143 (mmp-170) REVERT: A 309 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7558 (p90) outliers start: 9 outliers final: 3 residues processed: 28 average time/residue: 1.2868 time to fit residues: 37.6991 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.199 Angle : 0.510 6.434 7312 Z= 0.264 Chirality : 0.033 0.207 912 Planarity : 0.003 0.021 514 Dihedral : 22.125 82.735 2070 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.26 % Allowed : 15.35 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.49), residues: 292 helix: 2.07 (0.39), residues: 152 sheet: -1.55 (1.03), residues: 24 loop : -1.39 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.004 0.001 PHE A 197 TYR 0.027 0.002 TYR A 309 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.349 Fit side-chains REVERT: A 168 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7523 (mt-10) REVERT: A 223 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6065 (mmp-170) REVERT: A 309 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7389 (p90) outliers start: 7 outliers final: 1 residues processed: 29 average time/residue: 1.3643 time to fit residues: 41.2955 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5007 Z= 0.320 Angle : 0.585 7.061 7312 Z= 0.300 Chirality : 0.036 0.193 912 Planarity : 0.004 0.027 514 Dihedral : 22.166 83.264 2070 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.12 % Allowed : 16.28 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.48), residues: 292 helix: 1.78 (0.39), residues: 152 sheet: -1.57 (1.02), residues: 24 loop : -1.52 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 PHE 0.008 0.002 PHE A 197 TYR 0.033 0.002 TYR A 309 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.343 Fit side-chains REVERT: A 147 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.6852 (tm130) REVERT: A 168 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 223 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6150 (mmp-170) REVERT: A 309 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7590 (p90) outliers start: 11 outliers final: 4 residues processed: 30 average time/residue: 1.3326 time to fit residues: 41.6482 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.0570 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.161 Angle : 0.495 5.992 7312 Z= 0.257 Chirality : 0.032 0.219 912 Planarity : 0.003 0.020 514 Dihedral : 22.058 81.131 2070 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.26 % Allowed : 18.14 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.49), residues: 292 helix: 2.31 (0.39), residues: 152 sheet: -1.41 (1.03), residues: 24 loop : -1.46 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.006 0.001 PHE A 30 TYR 0.025 0.001 TYR A 309 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.338 Fit side-chains REVERT: A 147 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7111 (tm130) REVERT: A 168 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 213 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7910 (mtmm) REVERT: A 223 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6114 (mmp-170) REVERT: A 309 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7305 (p90) outliers start: 7 outliers final: 2 residues processed: 30 average time/residue: 1.2850 time to fit residues: 40.2097 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 10.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5007 Z= 0.405 Angle : 0.652 7.419 7312 Z= 0.332 Chirality : 0.039 0.196 912 Planarity : 0.005 0.034 514 Dihedral : 22.181 82.883 2070 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.26 % Allowed : 18.60 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.49), residues: 292 helix: 1.63 (0.39), residues: 152 sheet: -1.19 (0.83), residues: 34 loop : -1.59 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 313 HIS 0.005 0.002 HIS A 163 PHE 0.010 0.002 PHE A 197 TYR 0.036 0.002 TYR A 309 ARG 0.003 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.317 Fit side-chains REVERT: A 147 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.6586 (tm130) REVERT: A 168 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 223 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6167 (mmp-170) REVERT: A 309 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7689 (p90) REVERT: A 313 TRP cc_start: 0.7585 (m-10) cc_final: 0.5910 (m-10) outliers start: 7 outliers final: 4 residues processed: 30 average time/residue: 1.2409 time to fit residues: 38.8610 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.194 Angle : 0.522 6.141 7312 Z= 0.272 Chirality : 0.033 0.213 912 Planarity : 0.003 0.019 514 Dihedral : 22.072 81.829 2070 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 19.53 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.49), residues: 292 helix: 2.08 (0.39), residues: 152 sheet: -1.29 (1.06), residues: 24 loop : -1.44 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 70 HIS 0.004 0.002 HIS A 262 PHE 0.004 0.001 PHE A 30 TYR 0.027 0.001 TYR A 309 ARG 0.001 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.365 Fit side-chains REVERT: A 147 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.6883 (tm130) REVERT: A 168 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 223 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6060 (mmp-170) REVERT: A 309 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7402 (p90) outliers start: 5 outliers final: 1 residues processed: 27 average time/residue: 1.5701 time to fit residues: 44.0900 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5007 Z= 0.367 Angle : 0.626 7.234 7312 Z= 0.322 Chirality : 0.038 0.193 912 Planarity : 0.004 0.030 514 Dihedral : 22.136 82.115 2070 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.26 % Allowed : 19.07 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.48), residues: 292 helix: 1.64 (0.39), residues: 152 sheet: -1.11 (0.84), residues: 34 loop : -1.60 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 PHE 0.009 0.002 PHE A 197 TYR 0.034 0.002 TYR A 309 ARG 0.003 0.000 ARG A 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.330 Fit side-chains REVERT: A 147 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.6578 (tm130) REVERT: A 168 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 174 GLU cc_start: 0.6736 (mp0) cc_final: 0.6257 (mp0) REVERT: A 223 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6158 (mmp-170) REVERT: A 309 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7687 (p90) outliers start: 7 outliers final: 3 residues processed: 28 average time/residue: 1.3109 time to fit residues: 38.3953 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.207050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162844 restraints weight = 5099.432| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.34 r_work: 0.3743 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5007 Z= 0.192 Angle : 0.521 6.136 7312 Z= 0.271 Chirality : 0.033 0.214 912 Planarity : 0.003 0.017 514 Dihedral : 22.038 82.369 2070 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.86 % Allowed : 20.93 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.49), residues: 292 helix: 2.12 (0.39), residues: 152 sheet: -1.26 (1.04), residues: 24 loop : -1.48 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.004 0.002 HIS A 262 PHE 0.005 0.001 PHE A 30 TYR 0.026 0.001 TYR A 309 ARG 0.002 0.000 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1666.58 seconds wall clock time: 31 minutes 6.77 seconds (1866.77 seconds total)