Starting phenix.real_space_refine on Sun Mar 10 16:31:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcp_38250/03_2024/8xcp_38250_updated.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 3 5.49 5 S 14 5.16 5 C 2094 2.51 5 N 562 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 3309 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3255 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3247 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 394} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 415, 3247 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 394} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3311 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 54 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 13} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.12, per 1000 atoms: 1.25 Number of scatterers: 3309 At special positions: 0 Unit cell: (70.688, 69.184, 72.192, 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 14 16.00 P 3 15.00 O 636 8.00 N 562 7.00 C 2094 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: 1.09 Conformation dependent library (CDL) restraints added in 1.3 seconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 3 sheets defined 48.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 4.031A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.529A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.725A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.853A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.722A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.458A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.730A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 162 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1067 1.34 - 1.46: 671 1.46 - 1.58: 1604 1.58 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3371 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.567 0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" N ARG A 187 " pdb=" CA BARG A 187 " ideal model delta sigma weight residual 1.457 1.544 -0.087 1.32e-02 5.74e+03 4.39e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.441 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.435 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C8A NAP A 500 " pdb=" N7A NAP A 500 " ideal model delta sigma weight residual 1.301 1.397 -0.096 2.00e-02 2.50e+03 2.29e+01 ... (remaining 3366 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.24: 97 106.24 - 113.19: 1844 113.19 - 120.15: 1163 120.15 - 127.11: 1422 127.11 - 134.07: 52 Bond angle restraints: 4578 Sorted by residual: angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 118.85 124.90 -6.05 1.09e+00 8.42e-01 3.08e+01 angle pdb=" N ARG A 187 " pdb=" CA BARG A 187 " pdb=" C ARG A 187 " ideal model delta sigma weight residual 113.20 119.57 -6.37 1.21e+00 6.83e-01 2.77e+01 angle pdb=" N ARG A 187 " pdb=" CA AARG A 187 " pdb=" C ARG A 187 " ideal model delta sigma weight residual 113.20 118.35 -5.15 1.21e+00 6.83e-01 1.81e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.66 12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O1N NAP A 500 " pdb=" PN NAP A 500 " pdb=" O2N NAP A 500 " ideal model delta sigma weight residual 122.51 110.61 11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 4573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 1788 17.55 - 35.10: 176 35.10 - 52.64: 50 52.64 - 70.19: 17 70.19 - 87.74: 7 Dihedral angle restraints: 2038 sinusoidal: 846 harmonic: 1192 Sorted by residual: dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 -84.55 84.55 1 3.00e+01 1.11e-03 9.65e+00 dihedral pdb=" CA MET A 9 " pdb=" CB MET A 9 " pdb=" CG MET A 9 " pdb=" SD MET A 9 " ideal model delta sinusoidal sigma weight residual -60.00 -115.85 55.85 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CB LYS A 264 " pdb=" CG LYS A 264 " pdb=" CD LYS A 264 " pdb=" CE LYS A 264 " ideal model delta sinusoidal sigma weight residual 180.00 124.53 55.47 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 2035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 413 0.060 - 0.120: 76 0.120 - 0.181: 6 0.181 - 0.241: 1 0.241 - 0.301: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.45 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA AARG A 187 " pdb=" N ARG A 187 " pdb=" C ARG A 187 " pdb=" CB AARG A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CB VAL A 97 " pdb=" CA VAL A 97 " pdb=" CG1 VAL A 97 " pdb=" CG2 VAL A 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 494 not shown) Planarity restraints: 583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 346 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C GLY A 346 " 0.050 2.00e-02 2.50e+03 pdb=" O GLY A 346 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 347 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 150 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD BARG A 187 " 0.189 9.50e-02 1.11e+02 8.48e-02 4.41e+00 pdb=" NE BARG A 187 " -0.011 2.00e-02 2.50e+03 pdb=" CZ BARG A 187 " -0.003 2.00e-02 2.50e+03 pdb=" NH1BARG A 187 " -0.002 2.00e-02 2.50e+03 pdb=" NH2BARG A 187 " 0.007 2.00e-02 2.50e+03 ... (remaining 580 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1287 2.90 - 3.40: 3328 3.40 - 3.90: 5888 3.90 - 4.40: 6799 4.40 - 4.90: 11079 Nonbonded interactions: 28381 Sorted by model distance: nonbonded pdb=" N THR A 280 " pdb=" OE2 GLU A 283 " model vdw 2.405 2.520 nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.442 2.440 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 601 " model vdw 2.451 2.520 nonbonded pdb=" O LYS A 213 " pdb=" N THR A 238 " model vdw 2.458 2.520 nonbonded pdb=" OD1 ASP A 244 " pdb=" O3B NAP A 500 " model vdw 2.524 2.440 ... (remaining 28376 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=0.50 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.570 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.600 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.169 3371 Z= 0.551 Angle : 0.864 12.113 4578 Z= 0.477 Chirality : 0.048 0.301 497 Planarity : 0.006 0.085 583 Dihedral : 16.887 87.738 1278 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.97 % Allowed : 3.26 % Favored : 93.77 % 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 (0.42), residues: 414 helix: 1.60 (0.36), residues: 206 sheet: -1.12 (0.58), residues: 75 loop : -0.55 (0.58), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.407 Fit side-chains REVERT: A 9 MET cc_start: 0.6879 (tmm) cc_final: 0.6080 (tpt) REVERT: A 117 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7459 (mm-30) outliers start: 10 outliers final: 2 residues processed: 81 average time/residue: 1.2456 time to fit residues: 103.6359 Evaluate side-chains 53 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3371 Z= 0.162 Angle : 0.518 6.736 4578 Z= 0.266 Chirality : 0.042 0.150 497 Planarity : 0.004 0.048 583 Dihedral : 11.253 59.072 497 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.37 % Allowed : 13.06 % Favored : 84.57 % 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: 1.28 (0.43), residues: 414 helix: 2.15 (0.35), residues: 206 sheet: -0.50 (0.61), residues: 74 loop : -0.33 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.002 0.001 HIS A 75 PHE 0.007 0.001 PHE A 381 TYR 0.012 0.001 TYR A 363 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.379 Fit side-chains REVERT: A 9 MET cc_start: 0.6529 (tmm) cc_final: 0.5753 (tpt) REVERT: A 117 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7555 (mm-30) outliers start: 8 outliers final: 2 residues processed: 58 average time/residue: 1.2608 time to fit residues: 75.2521 Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 20.0000 chunk 11 optimal weight: 0.0030 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3371 Z= 0.135 Angle : 0.467 5.523 4578 Z= 0.240 Chirality : 0.041 0.137 497 Planarity : 0.004 0.048 583 Dihedral : 9.886 63.663 496 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.48 % Allowed : 14.54 % Favored : 83.98 % 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: 1.58 (0.43), residues: 414 helix: 2.34 (0.35), residues: 208 sheet: -0.32 (0.66), residues: 69 loop : -0.16 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.005 0.001 HIS A 388 PHE 0.006 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.378 Fit side-chains REVERT: A 9 MET cc_start: 0.6451 (tmm) cc_final: 0.5765 (tpt) REVERT: A 117 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 325 GLU cc_start: 0.6751 (tp30) cc_final: 0.6138 (tp30) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 1.3962 time to fit residues: 74.6201 Evaluate side-chains 43 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 333 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 281 ASN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3371 Z= 0.342 Angle : 0.552 5.553 4578 Z= 0.290 Chirality : 0.045 0.168 497 Planarity : 0.005 0.050 583 Dihedral : 9.905 54.223 496 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.08 % Allowed : 14.24 % Favored : 83.68 % 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: 1.19 (0.42), residues: 414 helix: 1.98 (0.34), residues: 208 sheet: -0.24 (0.63), residues: 74 loop : -0.45 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 364 HIS 0.002 0.001 HIS A 394 PHE 0.009 0.002 PHE A 381 TYR 0.018 0.002 TYR A 363 ARG 0.002 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.382 Fit side-chains REVERT: A 9 MET cc_start: 0.6572 (tmm) cc_final: 0.5804 (tpt) REVERT: A 12 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7184 (ttpp) REVERT: A 167 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8475 (mmtt) outliers start: 7 outliers final: 0 residues processed: 52 average time/residue: 1.4998 time to fit residues: 79.9657 Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 0.0030 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3371 Z= 0.198 Angle : 0.500 5.593 4578 Z= 0.259 Chirality : 0.043 0.137 497 Planarity : 0.005 0.049 583 Dihedral : 9.079 53.715 494 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.89 % Allowed : 16.62 % Favored : 82.49 % 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: 1.36 (0.42), residues: 414 helix: 2.14 (0.35), residues: 207 sheet: -0.15 (0.63), residues: 74 loop : -0.39 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.001 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.013 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.371 Fit side-chains REVERT: A 9 MET cc_start: 0.6524 (tmm) cc_final: 0.5760 (tpt) REVERT: A 12 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7228 (ttpp) REVERT: A 167 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8469 (mmtt) REVERT: A 310 LYS cc_start: 0.8066 (mttp) cc_final: 0.7580 (ptpp) REVERT: A 312 LYS cc_start: 0.8353 (mttm) cc_final: 0.7936 (mptt) outliers start: 3 outliers final: 0 residues processed: 55 average time/residue: 1.4489 time to fit residues: 81.7183 Evaluate side-chains 51 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3371 Z= 0.213 Angle : 0.522 5.560 4578 Z= 0.270 Chirality : 0.043 0.135 497 Planarity : 0.005 0.049 583 Dihedral : 8.814 53.653 494 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.59 % Allowed : 17.21 % Favored : 82.20 % 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: 1.46 (0.42), residues: 414 helix: 2.13 (0.35), residues: 207 sheet: 0.03 (0.68), residues: 69 loop : -0.27 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 30 HIS 0.001 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.012 0.001 TYR A 225 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.380 Fit side-chains REVERT: A 9 MET cc_start: 0.6510 (tmm) cc_final: 0.5745 (tpt) REVERT: A 12 LYS cc_start: 0.7588 (mtmt) cc_final: 0.7197 (ttpp) REVERT: A 167 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8480 (mmtt) REVERT: A 310 LYS cc_start: 0.8043 (mttp) cc_final: 0.7595 (ptpp) REVERT: A 312 LYS cc_start: 0.8374 (mttm) cc_final: 0.7960 (mptt) outliers start: 2 outliers final: 0 residues processed: 52 average time/residue: 1.4605 time to fit residues: 77.9813 Evaluate side-chains 50 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 3371 Z= 0.413 Angle : 0.613 5.917 4578 Z= 0.320 Chirality : 0.047 0.168 497 Planarity : 0.005 0.051 583 Dihedral : 9.592 54.410 494 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.78 % Allowed : 16.32 % Favored : 81.90 % 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: 0.98 (0.41), residues: 414 helix: 1.72 (0.35), residues: 207 sheet: 0.04 (0.64), residues: 74 loop : -0.64 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 364 HIS 0.003 0.001 HIS A 394 PHE 0.009 0.002 PHE A 381 TYR 0.018 0.002 TYR A 363 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.371 Fit side-chains REVERT: A 9 MET cc_start: 0.6582 (tmm) cc_final: 0.5811 (tpt) REVERT: A 12 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7204 (ttpp) REVERT: A 312 LYS cc_start: 0.8467 (mttm) cc_final: 0.8011 (mptt) outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 1.5208 time to fit residues: 85.7556 Evaluate side-chains 52 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3371 Z= 0.165 Angle : 0.516 6.058 4578 Z= 0.267 Chirality : 0.042 0.126 497 Planarity : 0.005 0.050 583 Dihedral : 8.532 54.514 494 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 18.10 % Favored : 81.90 % 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: 1.53 (0.42), residues: 414 helix: 2.16 (0.35), residues: 206 sheet: 0.30 (0.67), residues: 69 loop : -0.30 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.008 0.001 PHE A 381 TYR 0.013 0.001 TYR A 225 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.394 Fit side-chains REVERT: A 9 MET cc_start: 0.6457 (tmm) cc_final: 0.5727 (tpt) REVERT: A 310 LYS cc_start: 0.8244 (mttm) cc_final: 0.7941 (ptpt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.3756 time to fit residues: 72.1883 Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3371 Z= 0.194 Angle : 0.528 6.108 4578 Z= 0.272 Chirality : 0.043 0.127 497 Planarity : 0.005 0.050 583 Dihedral : 8.382 53.506 494 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % 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: 1.54 (0.42), residues: 414 helix: 2.18 (0.35), residues: 206 sheet: 0.19 (0.67), residues: 69 loop : -0.27 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.001 0.000 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.014 0.001 TYR A 225 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.389 Fit side-chains REVERT: A 9 MET cc_start: 0.6470 (tmm) cc_final: 0.5727 (tpt) REVERT: A 310 LYS cc_start: 0.8238 (mttm) cc_final: 0.7929 (ptpt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 1.5140 time to fit residues: 76.1827 Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3371 Z= 0.158 Angle : 0.516 6.716 4578 Z= 0.264 Chirality : 0.042 0.124 497 Planarity : 0.004 0.050 583 Dihedral : 8.037 54.408 494 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.30 % Allowed : 18.10 % Favored : 81.60 % 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: 1.68 (0.43), residues: 414 helix: 2.31 (0.35), residues: 206 sheet: 0.16 (0.68), residues: 69 loop : -0.15 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.001 0.000 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.012 0.001 TYR A 225 ARG 0.001 0.000 ARG A 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.383 Fit side-chains REVERT: A 9 MET cc_start: 0.6457 (tmm) cc_final: 0.5771 (tpt) REVERT: A 310 LYS cc_start: 0.8167 (mttm) cc_final: 0.7757 (ptpp) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 1.4003 time to fit residues: 72.0030 Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.085567 restraints weight = 10687.783| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.38 r_work: 0.2720 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3371 Z= 0.261 Angle : 0.552 6.396 4578 Z= 0.285 Chirality : 0.044 0.140 497 Planarity : 0.005 0.051 583 Dihedral : 8.445 54.033 494 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.30 % Allowed : 18.40 % Favored : 81.31 % 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: 1.53 (0.42), residues: 414 helix: 2.16 (0.35), residues: 206 sheet: 0.20 (0.67), residues: 69 loop : -0.25 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.002 0.001 HIS A 394 PHE 0.007 0.001 PHE A 381 TYR 0.015 0.002 TYR A 225 ARG 0.002 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.45 seconds wall clock time: 33 minutes 6.98 seconds (1986.98 seconds total)