Starting phenix.real_space_refine on Sun Mar 10 19:59:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/03_2024/8bf8_16016.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/03_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_16016/03_2024/8bf8_16016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/03_2024/8bf8_16016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/03_2024/8bf8_16016.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bf8_16016/03_2024/8bf8_16016.pdb" } 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 Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.45, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 448.4 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: 2.05 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: 1.90 Time building geometry restraints manager: 2.56 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: 100.20 - 106.95: 690 106.95 - 113.69: 2971 113.69 - 120.44: 1815 120.44 - 127.19: 1572 127.19 - 133.93: 264 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 2.440 nonbonded pdb=" NH2 ARG A 238 " pdb=" O6 G B -33 " model vdw 2.243 2.520 nonbonded pdb=" O2' A B -66 " pdb=" O2 C B -63 " model vdw 2.252 2.440 nonbonded pdb=" O2 C B-107 " pdb=" N2 G B -6 " model vdw 2.284 2.520 nonbonded pdb=" O LYS A 263 " pdb=" OG SER A 267 " model vdw 2.307 2.440 ... (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 ========== 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: 0.830 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: 4.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.670 Find NCS groups from input model: 0.100 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:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.329 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: 1.2134 time to fit residues: 44.2962 Evaluate side-chains 26 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5007 Z= 0.275 Angle : 0.550 6.608 7312 Z= 0.283 Chirality : 0.035 0.201 912 Planarity : 0.004 0.022 514 Dihedral : 22.296 86.547 2071 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.79 % Allowed : 13.95 % Favored : 83.26 % 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: 1.93 (0.40), residues: 152 sheet: -1.33 (1.26), residues: 21 loop : -0.93 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 70 HIS 0.004 0.002 HIS A 166 PHE 0.014 0.002 PHE A 35 TYR 0.032 0.002 TYR A 309 ARG 0.003 0.000 ARG A 110 *********************** 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 31 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.326 Fit side-chains REVERT: A 147 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.6879 (tm130) REVERT: A 168 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 174 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6439 (mt-10) REVERT: A 223 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6085 (mmp-170) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 1.2255 time to fit residues: 38.3773 Evaluate side-chains 30 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 265 THR Chi-restraints excluded: chain A residue 266 THR 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: 2.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 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: 0.8980 chunk 29 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5007 Z= 0.383 Angle : 0.633 7.411 7312 Z= 0.324 Chirality : 0.038 0.203 912 Planarity : 0.005 0.033 514 Dihedral : 22.349 85.352 2071 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.65 % Allowed : 14.42 % Favored : 80.93 % 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: 0.17 (0.49), residues: 292 helix: 1.50 (0.40), residues: 152 sheet: -1.77 (1.03), residues: 24 loop : -1.35 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 313 HIS 0.005 0.003 HIS A 163 PHE 0.009 0.002 PHE A 197 TYR 0.034 0.002 TYR A 309 ARG 0.003 0.001 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 38 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.331 Fit side-chains REVERT: A 80 GLN cc_start: 0.6892 (mt0) cc_final: 0.6627 (mt0) REVERT: A 168 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 174 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6472 (mt-10) REVERT: A 223 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6171 (mmp-170) REVERT: A 309 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7615 (p90) outliers start: 10 outliers final: 6 residues processed: 35 average time/residue: 1.1448 time to fit residues: 41.8490 Evaluate side-chains 36 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 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: 2.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 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: 1.7184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5007 Z= 0.366 Angle : 0.624 7.349 7312 Z= 0.320 Chirality : 0.038 0.204 912 Planarity : 0.005 0.030 514 Dihedral : 22.355 84.492 2071 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.51 % Allowed : 13.95 % Favored : 79.53 % 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: 0.11 (0.49), residues: 292 helix: 1.45 (0.39), residues: 152 sheet: -1.69 (1.03), residues: 24 loop : -1.42 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 313 HIS 0.005 0.002 HIS A 163 PHE 0.009 0.002 PHE A 197 TYR 0.031 0.002 TYR A 309 ARG 0.003 0.000 ARG A 160 *********************** 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 41 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 0.347 Fit side-chains REVERT: A 168 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 223 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6144 (mmp-170) REVERT: A 309 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7591 (p90) REVERT: A 313 TRP cc_start: 0.7562 (m-10) cc_final: 0.6049 (m-10) outliers start: 14 outliers final: 8 residues processed: 36 average time/residue: 1.0753 time to fit residues: 40.5623 Evaluate side-chains 36 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 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: 0.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5007 Z= 0.257 Angle : 0.556 6.811 7312 Z= 0.286 Chirality : 0.035 0.208 912 Planarity : 0.004 0.026 514 Dihedral : 22.212 82.684 2071 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.65 % Allowed : 16.28 % Favored : 79.07 % 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: 0.47 (0.49), residues: 292 helix: 1.80 (0.40), residues: 152 sheet: -1.61 (1.02), residues: 24 loop : -1.32 (0.57), 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 163 PHE 0.005 0.001 PHE A 197 TYR 0.031 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 35 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.338 Fit side-chains REVERT: A 110 ARG cc_start: 0.6237 (OUTLIER) cc_final: 0.5861 (mtt180) REVERT: A 168 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 223 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6083 (mmp-170) REVERT: A 309 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7489 (p90) outliers start: 10 outliers final: 5 residues processed: 32 average time/residue: 1.2905 time to fit residues: 43.0623 Evaluate side-chains 33 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 THR 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: 0.7980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1470 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= 0.219 Angle : 0.521 6.573 7312 Z= 0.268 Chirality : 0.034 0.210 912 Planarity : 0.004 0.024 514 Dihedral : 22.105 81.507 2071 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.05 % Allowed : 17.21 % Favored : 76.74 % 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: 0.67 (0.49), residues: 292 helix: 2.07 (0.40), residues: 152 sheet: -1.64 (1.00), residues: 24 loop : -1.36 (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 163 PHE 0.005 0.001 PHE A 197 TYR 0.028 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 41 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 28 time to evaluate : 0.312 Fit side-chains REVERT: A 110 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5824 (mtt180) REVERT: A 168 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 223 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6060 (mmp-170) REVERT: A 309 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7417 (p90) outliers start: 13 outliers final: 8 residues processed: 36 average time/residue: 1.2219 time to fit residues: 45.9255 Evaluate side-chains 38 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 27 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 THR 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: 10.0000 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1476 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= 0.214 Angle : 0.519 6.434 7312 Z= 0.267 Chirality : 0.033 0.209 912 Planarity : 0.004 0.024 514 Dihedral : 22.071 80.963 2071 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.05 % Allowed : 17.67 % Favored : 76.28 % 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: 0.71 (0.49), residues: 292 helix: 2.14 (0.40), residues: 152 sheet: -1.55 (1.01), residues: 24 loop : -1.41 (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 163 PHE 0.004 0.001 PHE A 197 TYR 0.029 0.002 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 40 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 27 time to evaluate : 0.339 Fit side-chains REVERT: A 110 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5811 (mtt180) REVERT: A 168 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 223 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6056 (mmp-170) REVERT: A 309 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7446 (p90) outliers start: 13 outliers final: 7 residues processed: 36 average time/residue: 1.1988 time to fit residues: 45.0292 Evaluate side-chains 37 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 THR 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: 0.5980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1698 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= 0.333 Angle : 0.603 7.272 7312 Z= 0.309 Chirality : 0.037 0.200 912 Planarity : 0.004 0.028 514 Dihedral : 22.189 81.846 2071 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.05 % Allowed : 18.14 % Favored : 75.81 % 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: 0.30 (0.48), residues: 292 helix: 1.73 (0.39), residues: 152 sheet: -1.68 (0.99), residues: 24 loop : -1.49 (0.56), residues: 116 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 0.008 0.002 PHE A 197 TYR 0.034 0.002 TYR A 309 ARG 0.003 0.000 ARG A 160 *********************** 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 37 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 24 time to evaluate : 0.330 Fit side-chains REVERT: A 110 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5884 (mtt180) REVERT: A 168 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 223 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6161 (mmp-170) REVERT: A 309 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7664 (p90) outliers start: 13 outliers final: 8 residues processed: 33 average time/residue: 1.1666 time to fit residues: 40.1993 Evaluate side-chains 35 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 24 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 110 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 THR 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: 2.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1594 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= 0.242 Angle : 0.554 8.838 7312 Z= 0.283 Chirality : 0.035 0.209 912 Planarity : 0.004 0.025 514 Dihedral : 22.108 80.480 2071 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.05 % Allowed : 18.14 % Favored : 75.81 % 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: 0.48 (0.48), residues: 292 helix: 1.97 (0.40), residues: 152 sheet: -1.63 (1.00), residues: 24 loop : -1.54 (0.55), 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 0.005 0.001 PHE A 197 TYR 0.029 0.002 TYR A 309 ARG 0.003 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 39 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.308 Fit side-chains REVERT: A 110 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5822 (mtt180) REVERT: A 168 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 223 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6126 (mmp-170) REVERT: A 309 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7426 (p90) outliers start: 13 outliers final: 10 residues processed: 36 average time/residue: 1.1407 time to fit residues: 42.8768 Evaluate side-chains 39 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 THR 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: 0.8980 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5007 Z= 0.342 Angle : 0.623 8.541 7312 Z= 0.316 Chirality : 0.038 0.236 912 Planarity : 0.004 0.027 514 Dihedral : 22.196 80.858 2071 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.51 % Allowed : 17.67 % Favored : 75.81 % 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: 0.29 (0.49), residues: 292 helix: 1.67 (0.39), residues: 152 sheet: -1.33 (0.82), residues: 39 loop : -1.46 (0.61), residues: 101 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 0.034 0.002 TYR A 309 ARG 0.003 0.000 ARG A 29 ********************** 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 38 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 24 time to evaluate : 0.330 Fit side-chains REVERT: A 110 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5895 (mtt180) REVERT: A 168 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 223 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6155 (mmp-170) REVERT: A 309 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7661 (p90) outliers start: 14 outliers final: 10 residues processed: 35 average time/residue: 1.2080 time to fit residues: 44.0996 Evaluate side-chains 37 residues out of total 255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 24 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 ILE 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 265 THR Chi-restraints excluded: chain A residue 266 THR 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: 0.0670 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.209530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.165791 restraints weight = 5098.520| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.37 r_work: 0.3787 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1633 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= 0.161 Angle : 0.508 8.806 7312 Z= 0.259 Chirality : 0.032 0.229 912 Planarity : 0.003 0.022 514 Dihedral : 21.973 77.494 2071 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.19 % Allowed : 19.53 % Favored : 76.28 % 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: 0.85 (0.50), residues: 292 helix: 2.39 (0.40), residues: 152 sheet: -1.34 (0.77), residues: 44 loop : -1.56 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.007 0.001 PHE A 30 TYR 0.024 0.001 TYR A 309 ARG 0.003 0.000 ARG A 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.74 seconds wall clock time: 28 minutes 41.79 seconds (1721.79 seconds total)