Starting phenix.real_space_refine on Mon Sep 23 20:57:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/09_2024/7t32_25648.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/09_2024/7t32_25648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/09_2024/7t32_25648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/09_2024/7t32_25648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/09_2024/7t32_25648.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t32_25648/09_2024/7t32_25648.cif" } resolution = 3.4 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= 0.002 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2829 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 1874 2.51 5 N 473 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2861 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2836 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 2830 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 66 Conformer: "B" Number of residues, atoms: 375, 2830 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 66 bond proxies already assigned to first conformer: 2883 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'ZMA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 35 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 35 " occ=0.40 Time building chain proxies: 4.23, per 1000 atoms: 1.48 Number of scatterers: 2861 At special positions: 0 Unit cell: (55.945, 78.49, 109.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 495 8.00 N 473 7.00 C 1874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 358 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 818.1 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.556A pdb=" N LEU A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP A 32 " --> pdb=" O CYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 69 removed outlier: 4.551A pdb=" N ILE A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 4.007A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 108 removed outlier: 4.849A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 4.722A pdb=" N ASN A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 142 Proline residue: A 139 - end of helix removed outlier: 4.265A pdb=" N GLY A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 182 through 227 Proline residue: A 189 - end of helix removed outlier: 4.096A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 250 Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.952A pdb=" N GLU A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 355 removed outlier: 3.987A pdb=" N THR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 362 through 387 removed outlier: 3.661A pdb=" N ASN A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.856A pdb=" N THR A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 735 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: 0.70 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 886 1.34 - 1.46: 408 1.46 - 1.57: 1606 1.57 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 2925 Sorted by residual: bond pdb=" C14 ZMA A1201 " pdb=" N15 ZMA A1201 " ideal model delta sigma weight residual 1.321 1.450 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C11 ZMA A1201 " pdb=" N10 ZMA A1201 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C20 ZMA A1201 " pdb=" C21 ZMA A1201 " ideal model delta sigma weight residual 1.442 1.526 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C18 ZMA A1201 " pdb=" N16 ZMA A1201 " ideal model delta sigma weight residual 1.372 1.294 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C18 ZMA A1201 " pdb=" N19 ZMA A1201 " ideal model delta sigma weight residual 1.320 1.388 -0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 2920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 3855 1.72 - 3.43: 104 3.43 - 5.15: 25 5.15 - 6.87: 8 6.87 - 8.58: 4 Bond angle restraints: 3996 Sorted by residual: angle pdb=" N VAL A 171 " pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 113.53 109.69 3.84 9.80e-01 1.04e+00 1.54e+01 angle pdb=" N GLU A 226 " pdb=" CA GLU A 226 " pdb=" CB GLU A 226 " ideal model delta sigma weight residual 110.28 116.02 -5.74 1.55e+00 4.16e-01 1.37e+01 angle pdb=" N VAL A 31 " pdb=" CA VAL A 31 " pdb=" C VAL A 31 " ideal model delta sigma weight residual 113.00 108.85 4.15 1.30e+00 5.92e-01 1.02e+01 angle pdb=" CA GLU A 226 " pdb=" CB GLU A 226 " pdb=" CG GLU A 226 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ASP A 229 " pdb=" N ASN A 230 " pdb=" CA ASN A 230 " ideal model delta sigma weight residual 121.54 127.48 -5.94 1.91e+00 2.74e-01 9.68e+00 ... (remaining 3991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 1523 16.31 - 32.61: 136 32.61 - 48.92: 32 48.92 - 65.23: 12 65.23 - 81.54: 2 Dihedral angle restraints: 1705 sinusoidal: 604 harmonic: 1101 Sorted by residual: dihedral pdb=" CB CYS A 77 " pdb=" SG CYS A 77 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 160.63 -67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA CYS A 185 " pdb=" C CYS A 185 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 315 0.030 - 0.060: 106 0.060 - 0.090: 40 0.090 - 0.120: 16 0.120 - 0.150: 3 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA GLU A 226 " pdb=" N GLU A 226 " pdb=" C GLU A 226 " pdb=" CB GLU A 226 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ASN A 230 " pdb=" N ASN A 230 " pdb=" C ASN A 230 " pdb=" CB ASN A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA GLN A 157 " pdb=" N GLN A 157 " pdb=" C GLN A 157 " pdb=" CB GLN A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 477 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 188 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO A 189 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 148 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 149 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 307 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.82e+00 pdb=" C ASN A 307 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 307 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 308 " 0.011 2.00e-02 2.50e+03 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 873 2.83 - 3.35: 3113 3.35 - 3.87: 4780 3.87 - 4.38: 4854 4.38 - 4.90: 8637 Nonbonded interactions: 22257 Sorted by model distance: nonbonded pdb=" NH1 ARG A 242 " pdb=" OD1 ASP A 281 " model vdw 2.313 3.120 nonbonded pdb=" O ALA A 231 " pdb=" N GLN A 233 " model vdw 2.321 3.120 nonbonded pdb=" O LEU A 222 " pdb=" OE1 GLU A 226 " model vdw 2.341 3.040 nonbonded pdb=" N GLU A 294 " pdb=" OE1 GLU A 294 " model vdw 2.359 3.120 nonbonded pdb=" O ALA A 134 " pdb=" OG1 THR A 138 " model vdw 2.363 3.040 ... (remaining 22252 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=0.40 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.006 0.129 2925 Z= 0.388 Angle : 0.774 8.585 3996 Z= 0.419 Chirality : 0.039 0.150 480 Planarity : 0.005 0.074 496 Dihedral : 14.073 81.537 982 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.12 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 1.86 (0.45), residues: 374 helix: 1.56 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.32 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 364 HIS 0.002 0.001 HIS A 155 PHE 0.018 0.001 PHE A 395 TYR 0.008 0.001 TYR A 384 ARG 0.002 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1343 time to fit residues: 9.5318 Evaluate side-chains 49 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2925 Z= 0.225 Angle : 0.668 8.710 3996 Z= 0.343 Chirality : 0.041 0.167 480 Planarity : 0.005 0.061 496 Dihedral : 5.757 72.665 399 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 0.70 % Allowed : 11.27 % Favored : 88.03 % 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: 2.17 (0.45), residues: 374 helix: 1.78 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.48 (0.93), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 364 HIS 0.002 0.001 HIS A 374 PHE 0.015 0.001 PHE A 62 TYR 0.030 0.002 TYR A 9 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8223 (t0) cc_final: 0.7993 (t0) REVERT: A 289 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7372 (mp0) REVERT: A 291 LYS cc_start: 0.7330 (mttt) cc_final: 0.7078 (mttt) REVERT: A 368 LEU cc_start: 0.8344 (tp) cc_final: 0.8009 (tt) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.1081 time to fit residues: 8.1583 Evaluate side-chains 53 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2925 Z= 0.210 Angle : 0.646 6.857 3996 Z= 0.331 Chirality : 0.041 0.205 480 Planarity : 0.005 0.051 496 Dihedral : 5.457 64.723 399 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 2.82 % Allowed : 13.73 % Favored : 83.45 % 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: 2.36 (0.45), residues: 374 helix: 1.91 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.49 (0.94), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.022 0.001 PHE A 182 TYR 0.020 0.002 TYR A 9 ARG 0.001 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 219 ASN cc_start: 0.8188 (t0) cc_final: 0.7942 (t0) REVERT: A 368 LEU cc_start: 0.8327 (tp) cc_final: 0.8051 (tt) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.1075 time to fit residues: 8.7142 Evaluate side-chains 58 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2925 Z= 0.236 Angle : 0.645 6.720 3996 Z= 0.330 Chirality : 0.041 0.196 480 Planarity : 0.004 0.047 496 Dihedral : 5.320 59.342 399 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.52 % Allowed : 14.44 % Favored : 82.04 % 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: 2.30 (0.45), residues: 374 helix: 1.86 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.44 (0.96), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 364 HIS 0.002 0.000 HIS A 326 PHE 0.012 0.001 PHE A 62 TYR 0.019 0.002 TYR A 384 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7730 (t80) REVERT: A 135 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8168 (mp) REVERT: A 219 ASN cc_start: 0.8195 (t0) cc_final: 0.7967 (t0) REVERT: A 340 LEU cc_start: 0.8219 (tt) cc_final: 0.7989 (tp) REVERT: A 368 LEU cc_start: 0.8316 (tp) cc_final: 0.8001 (tt) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.1017 time to fit residues: 8.4847 Evaluate side-chains 61 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 352 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2925 Z= 0.223 Angle : 0.639 6.640 3996 Z= 0.329 Chirality : 0.041 0.222 480 Planarity : 0.004 0.044 496 Dihedral : 5.230 55.970 399 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 3.52 % Allowed : 15.14 % Favored : 81.34 % 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: 2.35 (0.45), residues: 374 helix: 2.04 (0.30), residues: 315 sheet: None (None), residues: 0 loop : -1.12 (0.90), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.011 0.001 PHE A 62 TYR 0.016 0.001 TYR A 9 ARG 0.001 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 135 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 219 ASN cc_start: 0.8174 (t0) cc_final: 0.7908 (t0) REVERT: A 340 LEU cc_start: 0.8216 (tt) cc_final: 0.8001 (tp) REVERT: A 368 LEU cc_start: 0.8282 (tp) cc_final: 0.7969 (tt) REVERT: A 395 PHE cc_start: 0.6153 (m-80) cc_final: 0.5755 (m-10) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1013 time to fit residues: 8.5353 Evaluate side-chains 63 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2925 Z= 0.219 Angle : 0.650 9.646 3996 Z= 0.328 Chirality : 0.041 0.232 480 Planarity : 0.004 0.042 496 Dihedral : 5.151 53.395 399 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 3.17 % Allowed : 16.55 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.45), residues: 374 helix: 1.93 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.34 (0.97), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.011 0.001 PHE A 62 TYR 0.016 0.001 TYR A 384 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 135 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 219 ASN cc_start: 0.8192 (t0) cc_final: 0.7926 (t0) REVERT: A 340 LEU cc_start: 0.8213 (tt) cc_final: 0.8005 (tp) REVERT: A 368 LEU cc_start: 0.8276 (tp) cc_final: 0.7965 (tt) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.1004 time to fit residues: 8.0180 Evaluate side-chains 63 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2925 Z= 0.231 Angle : 0.652 9.551 3996 Z= 0.328 Chirality : 0.041 0.199 480 Planarity : 0.004 0.041 496 Dihedral : 5.135 51.614 399 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 3.52 % Allowed : 16.55 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.45), residues: 374 helix: 1.90 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.34 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.011 0.001 PHE A 62 TYR 0.017 0.001 TYR A 9 ARG 0.001 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7714 (t80) REVERT: A 135 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 219 ASN cc_start: 0.8173 (t0) cc_final: 0.7918 (t0) REVERT: A 340 LEU cc_start: 0.8195 (tt) cc_final: 0.7992 (tp) REVERT: A 368 LEU cc_start: 0.8259 (tp) cc_final: 0.7960 (tt) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.0974 time to fit residues: 7.9842 Evaluate side-chains 63 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2925 Z= 0.221 Angle : 0.659 9.666 3996 Z= 0.333 Chirality : 0.041 0.229 480 Planarity : 0.004 0.039 496 Dihedral : 5.078 49.832 399 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.50 % Favored : 96.23 % Rotamer: Outliers : 3.52 % Allowed : 17.61 % Favored : 78.87 % 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: 2.41 (0.45), residues: 374 helix: 1.96 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.53 (0.91), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 364 HIS 0.001 0.000 HIS A 326 PHE 0.010 0.001 PHE A 62 TYR 0.016 0.002 TYR A 384 ARG 0.001 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7732 (t80) REVERT: A 135 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8409 (mp) REVERT: A 219 ASN cc_start: 0.8161 (t0) cc_final: 0.7879 (t0) REVERT: A 340 LEU cc_start: 0.8179 (tt) cc_final: 0.7978 (tp) REVERT: A 368 LEU cc_start: 0.8288 (tp) cc_final: 0.7957 (tt) REVERT: A 395 PHE cc_start: 0.6207 (m-80) cc_final: 0.5775 (m-10) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.1035 time to fit residues: 8.2705 Evaluate side-chains 60 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2925 Z= 0.219 Angle : 0.664 9.606 3996 Z= 0.333 Chirality : 0.042 0.247 480 Planarity : 0.004 0.039 496 Dihedral : 5.047 48.604 399 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.52 % Allowed : 17.25 % Favored : 79.23 % 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: 2.42 (0.45), residues: 374 helix: 1.98 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.64 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.018 0.001 PHE A 182 TYR 0.016 0.002 TYR A 103 ARG 0.001 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7794 (t80) REVERT: A 135 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 219 ASN cc_start: 0.8151 (t0) cc_final: 0.7841 (t0) REVERT: A 340 LEU cc_start: 0.8174 (tt) cc_final: 0.7972 (tp) REVERT: A 368 LEU cc_start: 0.8188 (tp) cc_final: 0.7866 (tt) REVERT: A 395 PHE cc_start: 0.6227 (m-80) cc_final: 0.5901 (m-10) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.0957 time to fit residues: 7.2773 Evaluate side-chains 59 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2925 Z= 0.231 Angle : 0.667 9.552 3996 Z= 0.337 Chirality : 0.041 0.214 480 Planarity : 0.004 0.039 496 Dihedral : 5.020 47.748 399 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.96 % Favored : 96.77 % Rotamer: Outliers : 3.87 % Allowed : 17.25 % Favored : 78.87 % 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: 2.36 (0.45), residues: 374 helix: 1.94 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.73 (0.88), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 364 HIS 0.001 0.000 HIS A 75 PHE 0.010 0.001 PHE A 62 TYR 0.015 0.001 TYR A 9 ARG 0.001 0.000 ARG A 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7760 (t80) REVERT: A 135 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 219 ASN cc_start: 0.8162 (t0) cc_final: 0.7881 (t0) REVERT: A 340 LEU cc_start: 0.8209 (tt) cc_final: 0.8006 (tp) REVERT: A 368 LEU cc_start: 0.8184 (tp) cc_final: 0.7863 (tt) REVERT: A 395 PHE cc_start: 0.6214 (m-80) cc_final: 0.5918 (m-10) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.1109 time to fit residues: 8.3988 Evaluate side-chains 61 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.164000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130753 restraints weight = 19113.066| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 7.83 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.003 0.033 2925 Z= 0.206 Angle : 0.651 9.889 3996 Z= 0.327 Chirality : 0.041 0.276 480 Planarity : 0.004 0.038 496 Dihedral : 4.947 45.500 399 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 3.52 % Allowed : 17.61 % Favored : 78.87 % 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: 2.45 (0.45), residues: 374 helix: 1.99 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -0.62 (0.90), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 364 HIS 0.001 0.000 HIS A 346 PHE 0.019 0.001 PHE A 182 TYR 0.017 0.002 TYR A 103 ARG 0.001 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1010.88 seconds wall clock time: 18 minutes 34.32 seconds (1114.32 seconds total)