Starting phenix.real_space_refine on Wed Jan 17 13:14:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcz_38260/01_2024/8xcz_38260_neut_updated.pdb" } resolution = 2.83 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 2 5.49 5 S 14 5.16 5 C 2107 2.51 5 N 563 2.21 5 O 638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3270 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3251 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 416, 3251 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3301 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 54 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 17} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 46 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: 4.17, per 1000 atoms: 1.25 Number of scatterers: 3324 At special positions: 0 Unit cell: (66.928, 72.944, 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 2 15.00 O 638 8.00 N 563 7.00 C 2107 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: 1.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 4 sheets defined 47.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.732A 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 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: 5.662A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.123A 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 205 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 285 Processing helix chain 'A' and resid 324 through 333 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: 4.694A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 68 through 71 Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.834A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 7.098A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 166 hydrogen bonds defined for protein. 482 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: 0.94 Time building geometry restraints manager: 1.37 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: 1072 1.34 - 1.46: 679 1.46 - 1.58: 1605 1.58 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3385 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.568 0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" C TRP A 89 " pdb=" CA BTRP A 89 " ideal model delta sigma weight residual 1.524 1.618 -0.094 1.29e-02 6.01e+03 5.34e+01 bond pdb=" C ARG A 187 " pdb=" CA BARG A 187 " ideal model delta sigma weight residual 1.522 1.439 0.084 1.37e-02 5.33e+03 3.73e+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 2.95e+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 ... (remaining 3380 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 112 106.64 - 113.50: 1858 113.50 - 120.35: 1195 120.35 - 127.20: 1386 127.20 - 134.05: 49 Bond angle restraints: 4600 Sorted by residual: angle pdb=" N TRP A 89 " pdb=" CA BTRP A 89 " pdb=" C TRP A 89 " ideal model delta sigma weight residual 111.36 105.20 6.16 1.09e+00 8.42e-01 3.20e+01 angle pdb=" N GLN A 234 " pdb=" CA GLN A 234 " pdb=" C GLN A 234 " ideal model delta sigma weight residual 111.36 116.90 -5.54 1.09e+00 8.42e-01 2.59e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.68 12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 119.05 123.49 -4.44 1.11e+00 8.12e-01 1.60e+01 angle pdb=" C HIS A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 119.19 122.56 -3.37 1.06e+00 8.90e-01 1.01e+01 ... (remaining 4595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 1777 17.14 - 34.29: 179 34.29 - 51.43: 52 51.43 - 68.57: 21 68.57 - 85.71: 10 Dihedral angle restraints: 2039 sinusoidal: 840 harmonic: 1199 Sorted by residual: dihedral pdb=" CA AARG A 187 " pdb=" CB AARG A 187 " pdb=" CG AARG A 187 " pdb=" CD AARG A 187 " ideal model delta sinusoidal sigma weight residual -60.00 -119.21 59.21 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG A 246 " pdb=" CA ARG A 246 " pdb=" CB ARG A 246 " pdb=" CG ARG A 246 " ideal model delta sinusoidal sigma weight residual -180.00 -121.51 -58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLU A 78 " pdb=" CA GLU A 78 " pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " ideal model delta sinusoidal sigma weight residual -60.00 -117.65 57.65 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 426 0.060 - 0.119: 62 0.119 - 0.179: 9 0.179 - 0.239: 2 0.239 - 0.298: 1 Chirality restraints: 500 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 -2.46 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA BTRP A 89 " pdb=" N TRP A 89 " pdb=" C TRP A 89 " pdb=" CB BTRP A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ASP A 272 " pdb=" N ASP A 272 " pdb=" C ASP A 272 " pdb=" CB ASP A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 497 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG A 187 " 0.225 9.50e-02 1.11e+02 1.01e-01 6.25e+00 pdb=" NE BARG A 187 " -0.013 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 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 150 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 142 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.020 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1341 2.92 - 3.42: 3331 3.42 - 3.91: 5938 3.91 - 4.41: 6672 4.41 - 4.90: 10986 Nonbonded interactions: 28268 Sorted by model distance: nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.428 2.440 nonbonded pdb=" O THR A 323 " pdb=" N ASP A 327 " model vdw 2.459 2.520 nonbonded pdb=" OG SER A 243 " pdb=" O GLY A 247 " model vdw 2.462 2.440 nonbonded pdb=" O ASP A 413 " pdb=" O HOH A 601 " model vdw 2.489 2.440 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.495 2.520 ... (remaining 28263 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=0.99 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: 0.610 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: 3.470 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 3385 Z= 0.479 Angle : 0.742 12.088 4600 Z= 0.417 Chirality : 0.047 0.298 500 Planarity : 0.006 0.101 586 Dihedral : 17.165 85.713 1275 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.85 % Allowed : 2.96 % Favored : 93.20 % 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: 1.41 (0.42), residues: 416 helix: 2.35 (0.34), residues: 211 sheet: -0.64 (0.66), residues: 70 loop : -0.41 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.006 0.001 PHE A 341 TYR 0.006 0.001 TYR A 408 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.405 Fit side-chains REVERT: A 78 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 332 GLU cc_start: 0.7904 (tp30) cc_final: 0.7699 (tm-30) REVERT: A 419 LYS cc_start: 0.7546 (mttt) cc_final: 0.7293 (mttm) outliers start: 12 outliers final: 2 residues processed: 59 average time/residue: 1.4130 time to fit residues: 85.5312 Evaluate side-chains 43 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 237 MET 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: 20.0000 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 222 ASN A 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3385 Z= 0.135 Angle : 0.434 6.123 4600 Z= 0.227 Chirality : 0.041 0.141 500 Planarity : 0.004 0.047 586 Dihedral : 10.936 66.066 499 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.18 % Allowed : 10.65 % Favored : 88.17 % 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: 1.67 (0.43), residues: 416 helix: 2.37 (0.34), residues: 215 sheet: -0.17 (0.68), residues: 72 loop : -0.25 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.006 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.369 Fit side-chains REVERT: A 78 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: A 419 LYS cc_start: 0.7572 (mttt) cc_final: 0.7307 (mttm) outliers start: 3 outliers final: 0 residues processed: 45 average time/residue: 1.3352 time to fit residues: 61.9136 Evaluate side-chains 42 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3385 Z= 0.141 Angle : 0.421 5.434 4600 Z= 0.220 Chirality : 0.041 0.134 500 Planarity : 0.004 0.047 586 Dihedral : 9.879 71.815 494 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.48 % Allowed : 11.54 % Favored : 86.98 % 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: 1.80 (0.42), residues: 416 helix: 2.44 (0.34), residues: 214 sheet: 0.48 (0.74), residues: 60 loop : -0.44 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.405 Fit side-chains REVERT: A 78 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: A 419 LYS cc_start: 0.7604 (mttt) cc_final: 0.7400 (mttm) outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 1.1530 time to fit residues: 54.8231 Evaluate side-chains 41 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3385 Z= 0.201 Angle : 0.457 5.588 4600 Z= 0.237 Chirality : 0.043 0.135 500 Planarity : 0.004 0.048 586 Dihedral : 9.793 73.383 494 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.18 % Allowed : 12.43 % Favored : 86.39 % 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: 1.67 (0.42), residues: 416 helix: 2.42 (0.34), residues: 213 sheet: 0.24 (0.72), residues: 62 loop : -0.54 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 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: 3 poor density : 46 time to evaluate : 0.385 Fit side-chains REVERT: A 78 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: A 251 ASN cc_start: 0.7437 (t0) cc_final: 0.7055 (t0) REVERT: A 287 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8648 (tm) REVERT: A 419 LYS cc_start: 0.7673 (mttt) cc_final: 0.7391 (mttm) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 1.2250 time to fit residues: 59.4406 Evaluate side-chains 46 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.0170 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3385 Z= 0.110 Angle : 0.447 9.464 4600 Z= 0.222 Chirality : 0.041 0.123 500 Planarity : 0.004 0.047 586 Dihedral : 9.079 75.063 494 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.78 % Allowed : 13.91 % Favored : 84.32 % 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: 1.83 (0.42), residues: 416 helix: 2.52 (0.34), residues: 215 sheet: 0.32 (0.72), residues: 62 loop : -0.45 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.001 0.000 HIS A 75 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 160 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 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: 5 poor density : 48 time to evaluate : 0.382 Fit side-chains REVERT: A 78 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: A 287 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8604 (tm) REVERT: A 379 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8565 (ttpt) REVERT: A 419 LYS cc_start: 0.7536 (mttt) cc_final: 0.7331 (mttm) outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 1.2361 time to fit residues: 62.5298 Evaluate side-chains 49 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN A 251 ASN A 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3385 Z= 0.145 Angle : 0.440 5.075 4600 Z= 0.226 Chirality : 0.042 0.123 500 Planarity : 0.004 0.048 586 Dihedral : 8.746 75.742 494 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.18 % Allowed : 15.38 % Favored : 83.43 % 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: 1.83 (0.42), residues: 416 helix: 2.49 (0.34), residues: 214 sheet: 0.33 (0.72), residues: 62 loop : -0.38 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.389 Fit side-chains REVERT: A 78 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: A 287 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8566 (tm) REVERT: A 379 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8562 (ttpt) REVERT: A 419 LYS cc_start: 0.7608 (mttt) cc_final: 0.7399 (mttm) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 1.2153 time to fit residues: 57.7641 Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3385 Z= 0.327 Angle : 0.517 5.882 4600 Z= 0.268 Chirality : 0.045 0.141 500 Planarity : 0.005 0.050 586 Dihedral : 9.121 82.947 494 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.48 % Allowed : 14.79 % Favored : 83.73 % 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: 1.52 (0.42), residues: 416 helix: 2.17 (0.34), residues: 214 sheet: 0.09 (0.68), residues: 67 loop : -0.36 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.002 0.001 HIS A 61 PHE 0.009 0.001 PHE A 381 TYR 0.011 0.001 TYR A 363 ARG 0.004 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.389 Fit side-chains REVERT: A 287 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8621 (tm) REVERT: A 419 LYS cc_start: 0.7794 (mttt) cc_final: 0.7567 (mttm) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 1.2896 time to fit residues: 59.8704 Evaluate side-chains 44 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3385 Z= 0.168 Angle : 0.459 5.472 4600 Z= 0.238 Chirality : 0.043 0.126 500 Planarity : 0.005 0.049 586 Dihedral : 9.069 84.184 494 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.18 % Allowed : 14.50 % Favored : 84.32 % 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: 1.56 (0.42), residues: 416 helix: 2.25 (0.34), residues: 214 sheet: 0.19 (0.70), residues: 62 loop : -0.45 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.010 0.001 PHE A 381 TYR 0.009 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.411 Fit side-chains REVERT: A 78 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: A 287 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8591 (tm) REVERT: A 379 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8539 (ttpt) REVERT: A 419 LYS cc_start: 0.7650 (mttt) cc_final: 0.7426 (mttm) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 1.2791 time to fit residues: 59.4151 Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3385 Z= 0.218 Angle : 0.478 5.552 4600 Z= 0.248 Chirality : 0.044 0.128 500 Planarity : 0.005 0.049 586 Dihedral : 9.117 86.044 494 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.18 % Allowed : 15.09 % Favored : 83.73 % 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: 1.52 (0.42), residues: 416 helix: 2.21 (0.34), residues: 214 sheet: 0.17 (0.70), residues: 62 loop : -0.46 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.386 Fit side-chains REVERT: A 78 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: A 287 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8588 (tm) REVERT: A 379 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8546 (ttpt) REVERT: A 419 LYS cc_start: 0.7712 (mttt) cc_final: 0.7426 (mttm) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 1.2300 time to fit residues: 57.1882 Evaluate side-chains 46 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 287 LEU 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: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.0000 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3385 Z= 0.118 Angle : 0.434 4.968 4600 Z= 0.225 Chirality : 0.042 0.129 500 Planarity : 0.004 0.049 586 Dihedral : 8.855 84.547 494 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.48 % Allowed : 15.09 % Favored : 83.43 % 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: 1.67 (0.42), residues: 416 helix: 2.30 (0.34), residues: 216 sheet: 0.28 (0.71), residues: 62 loop : -0.40 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 160 ARG 0.004 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.396 Fit side-chains REVERT: A 78 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: A 287 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8577 (tm) REVERT: A 332 GLU cc_start: 0.7848 (tp30) cc_final: 0.7646 (tm-30) REVERT: A 379 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8529 (ttpt) REVERT: A 419 LYS cc_start: 0.7557 (mttt) cc_final: 0.7287 (mttm) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 1.3338 time to fit residues: 61.8887 Evaluate side-chains 48 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.0060 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.093184 restraints weight = 7853.459| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.31 r_work: 0.2764 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3385 Z= 0.227 Angle : 0.475 5.539 4600 Z= 0.247 Chirality : 0.044 0.129 500 Planarity : 0.005 0.049 586 Dihedral : 9.043 86.170 494 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.78 % Allowed : 15.38 % Favored : 82.84 % 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: 1.62 (0.42), residues: 416 helix: 2.29 (0.34), residues: 214 sheet: 0.20 (0.70), residues: 62 loop : -0.41 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 61 PHE 0.008 0.001 PHE A 381 TYR 0.011 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.65 seconds wall clock time: 32 minutes 27.16 seconds (1947.16 seconds total)