Starting phenix.real_space_refine on Mon Sep 23 16:54:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/09_2024/7fij_31599.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/09_2024/7fij_31599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/09_2024/7fij_31599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/09_2024/7fij_31599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/09_2024/7fij_31599.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/09_2024/7fij_31599.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 1212 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 4 5.16 5 C 1865 2.51 5 N 594 2.21 5 O 598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3061 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3061 Classifications: {'peptide': 561} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 412} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 534} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1442 Unresolved non-hydrogen angles: 1848 Unresolved non-hydrogen dihedrals: 1194 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 34, 'GLU:plan': 23, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 673 Time building chain proxies: 2.62, per 1000 atoms: 0.86 Number of scatterers: 3061 At special positions: 0 Unit cell: (61.655, 81.51, 124.355, 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 4 16.00 O 598 8.00 N 594 7.00 C 1865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " 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: 0.74 Conformation dependent library (CDL) restraints added in 460.7 milliseconds 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 43.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'R' and resid 241 through 245 removed outlier: 4.068A pdb=" N SER R 244 " --> pdb=" O GLY R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 362 through 387 removed outlier: 3.961A pdb=" N ILE R 366 " --> pdb=" O LEU R 362 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 420 Processing helix chain 'R' and resid 429 through 435 removed outlier: 3.531A pdb=" N THR R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 468 removed outlier: 3.717A pdb=" N ARG R 464 " --> pdb=" O ILE R 460 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP R 465 " --> pdb=" O THR R 461 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS R 466 " --> pdb=" O LEU R 462 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE R 468 " --> pdb=" O ARG R 464 " (cutoff:3.500A) Processing helix chain 'R' and resid 470 through 477 removed outlier: 5.409A pdb=" N ASP R 475 " --> pdb=" O ILE R 472 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 504 Proline residue: R 501 - end of helix removed outlier: 3.772A pdb=" N GLY R 504 " --> pdb=" O LEU R 500 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 552 Processing helix chain 'R' and resid 560 through 595 removed outlier: 3.555A pdb=" N CYS R 581 " --> pdb=" O THR R 577 " (cutoff:3.500A) Proline residue: R 584 - end of helix Processing helix chain 'R' and resid 603 through 610 removed outlier: 3.679A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU R 608 " --> pdb=" O SER R 604 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 624 removed outlier: 4.118A pdb=" N CYS R 617 " --> pdb=" O PRO R 613 " (cutoff:3.500A) Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 641 Processing sheet with id=AA1, first strand: chain 'R' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'R' and resid 102 through 105 removed outlier: 6.336A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 163 through 164 removed outlier: 4.163A pdb=" N ILE R 164 " --> pdb=" O GLU R 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'R' and resid 226 through 228 185 hydrogen bonds defined for protein. 537 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: 0.91 Time building geometry restraints manager: 0.92 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: 1173 1.34 - 1.46: 569 1.46 - 1.58: 1335 1.58 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3083 Sorted by residual: bond pdb=" CB PRO R 345 " pdb=" CG PRO R 345 " ideal model delta sigma weight residual 1.506 1.484 0.022 3.90e-02 6.57e+02 3.09e-01 bond pdb=" C SER R 512 " pdb=" N ILE R 513 " ideal model delta sigma weight residual 1.338 1.332 0.006 1.01e-02 9.80e+03 3.08e-01 bond pdb=" C VAL R 393 " pdb=" N PRO R 394 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.57e-01 bond pdb=" CA TYR R 612 " pdb=" C TYR R 612 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.44e-01 bond pdb=" CA TYR R 275 " pdb=" CB TYR R 275 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.71e-02 3.42e+03 2.24e-01 ... (remaining 3078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 4246 1.64 - 3.28: 23 3.28 - 4.91: 8 4.91 - 6.55: 1 6.55 - 8.19: 1 Bond angle restraints: 4279 Sorted by residual: angle pdb=" N ILE R 513 " pdb=" CA ILE R 513 " pdb=" C ILE R 513 " ideal model delta sigma weight residual 112.98 109.68 3.30 1.25e+00 6.40e-01 6.95e+00 angle pdb=" CA LEU R 122 " pdb=" CB LEU R 122 " pdb=" CG LEU R 122 " ideal model delta sigma weight residual 116.30 124.49 -8.19 3.50e+00 8.16e-02 5.47e+00 angle pdb=" N ASN R 132 " pdb=" CA ASN R 132 " pdb=" CB ASN R 132 " ideal model delta sigma weight residual 113.65 110.34 3.31 1.47e+00 4.63e-01 5.06e+00 angle pdb=" C SER R 253 " pdb=" N TYR R 254 " pdb=" CA TYR R 254 " ideal model delta sigma weight residual 121.54 125.21 -3.67 1.91e+00 2.74e-01 3.70e+00 angle pdb=" N ILE R 625 " pdb=" CA ILE R 625 " pdb=" C ILE R 625 " ideal model delta sigma weight residual 109.34 112.81 -3.47 2.08e+00 2.31e-01 2.78e+00 ... (remaining 4274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.22: 1752 14.22 - 28.44: 40 28.44 - 42.66: 12 42.66 - 56.88: 0 56.88 - 71.10: 3 Dihedral angle restraints: 1807 sinusoidal: 175 harmonic: 1632 Sorted by residual: dihedral pdb=" CB CYS R 439 " pdb=" SG CYS R 439 " pdb=" SG CYS R 514 " pdb=" CB CYS R 514 " ideal model delta sinusoidal sigma weight residual 93.00 31.48 61.52 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" N ASN R 207 " pdb=" CA ASN R 207 " pdb=" CB ASN R 207 " pdb=" CG ASN R 207 " ideal model delta sinusoidal sigma weight residual -180.00 -141.07 -38.93 3 1.50e+01 4.44e-03 6.88e+00 dihedral pdb=" CA ALA R 560 " pdb=" C ALA R 560 " pdb=" N THR R 561 " pdb=" CA THR R 561 " ideal model delta harmonic sigma weight residual -180.00 -167.09 -12.91 0 5.00e+00 4.00e-02 6.67e+00 ... (remaining 1804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 307 0.026 - 0.053: 146 0.053 - 0.079: 67 0.079 - 0.106: 30 0.106 - 0.132: 12 Chirality restraints: 562 Sorted by residual: chirality pdb=" CA ILE R 64 " pdb=" N ILE R 64 " pdb=" C ILE R 64 " pdb=" CB ILE R 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE R 78 " pdb=" N ILE R 78 " pdb=" C ILE R 78 " pdb=" CB ILE R 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE R 155 " pdb=" N ILE R 155 " pdb=" C ILE R 155 " pdb=" CB ILE R 155 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 559 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 612 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.62e-01 pdb=" N PRO R 613 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO R 613 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO R 613 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 561 " 0.003 2.00e-02 2.50e+03 5.22e-03 2.72e-01 pdb=" C THR R 561 " -0.009 2.00e-02 2.50e+03 pdb=" O THR R 561 " 0.003 2.00e-02 2.50e+03 pdb=" N ASN R 562 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 579 " 0.002 2.00e-02 2.50e+03 4.55e-03 2.07e-01 pdb=" C PHE R 579 " -0.008 2.00e-02 2.50e+03 pdb=" O PHE R 579 " 0.003 2.00e-02 2.50e+03 pdb=" N THR R 580 " 0.003 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 1194 2.86 - 3.37: 2958 3.37 - 3.88: 4765 3.88 - 4.39: 4448 4.39 - 4.90: 8351 Nonbonded interactions: 21716 Sorted by model distance: nonbonded pdb=" O THR R 133 " pdb=" ND2 ASN R 158 " model vdw 2.344 3.120 nonbonded pdb=" O ILE R 76 " pdb=" N SER R 101 " model vdw 2.398 3.120 nonbonded pdb=" O LEU R 638 " pdb=" N CYS R 644 " model vdw 2.402 3.120 nonbonded pdb=" O ASP R 419 " pdb=" OG1 THR R 422 " model vdw 2.406 3.040 nonbonded pdb=" N ILE R 229 " pdb=" O ILE R 249 " model vdw 2.411 3.120 ... (remaining 21711 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5027 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 : 0.001 0.022 3083 Z= 0.094 Angle : 0.412 8.189 4279 Z= 0.237 Chirality : 0.042 0.132 562 Planarity : 0.001 0.019 603 Dihedral : 8.017 71.101 736 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.10 (0.39), residues: 557 helix: 3.63 (0.34), residues: 214 sheet: -1.28 (0.74), residues: 49 loop : -1.24 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 367 HIS 0.001 0.000 HIS R 278 PHE 0.003 0.000 PHE R 265 TYR 0.006 0.001 TYR R 427 ARG 0.001 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.311 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0701 time to fit residues: 3.8167 Evaluate side-chains 35 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.5316 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.228 Angle : 0.512 7.588 4279 Z= 0.298 Chirality : 0.045 0.187 562 Planarity : 0.003 0.035 603 Dihedral : 4.263 18.769 567 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.00 % Allowed : 7.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.38), residues: 557 helix: 3.18 (0.35), residues: 210 sheet: -1.39 (0.77), residues: 47 loop : -1.46 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 367 HIS 0.003 0.002 HIS R 214 PHE 0.014 0.001 PHE R 265 TYR 0.009 0.001 TYR R 359 ARG 0.012 0.003 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.268 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0794 time to fit residues: 4.5584 Evaluate side-chains 39 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.5470 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3083 Z= 0.293 Angle : 0.584 7.139 4279 Z= 0.345 Chirality : 0.046 0.147 562 Planarity : 0.003 0.035 603 Dihedral : 5.492 21.592 567 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.50 % Allowed : 22.50 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.38), residues: 557 helix: 2.55 (0.35), residues: 209 sheet: -1.64 (0.80), residues: 47 loop : -1.89 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 367 HIS 0.007 0.002 HIS R 214 PHE 0.023 0.002 PHE R 265 TYR 0.009 0.001 TYR R 427 ARG 0.015 0.003 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.301 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.0668 time to fit residues: 3.9789 Evaluate side-chains 38 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3083 Z= 0.242 Angle : 0.537 6.151 4279 Z= 0.316 Chirality : 0.046 0.172 562 Planarity : 0.003 0.031 603 Dihedral : 5.435 19.671 567 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 10.00 % Allowed : 21.25 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.38), residues: 557 helix: 2.71 (0.35), residues: 203 sheet: -1.82 (0.82), residues: 47 loop : -1.99 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 491 HIS 0.005 0.003 HIS R 214 PHE 0.022 0.001 PHE R 265 TYR 0.014 0.002 TYR R 427 ARG 0.011 0.002 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.287 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 40 average time/residue: 0.0660 time to fit residues: 4.1304 Evaluate side-chains 42 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 31 optimal weight: 5.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3083 Z= 0.326 Angle : 0.630 7.405 4279 Z= 0.374 Chirality : 0.048 0.155 562 Planarity : 0.004 0.034 603 Dihedral : 6.346 20.790 567 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 8.75 % Allowed : 25.00 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.37), residues: 557 helix: 2.02 (0.35), residues: 214 sheet: -2.08 (0.84), residues: 45 loop : -2.45 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 491 HIS 0.008 0.003 HIS R 214 PHE 0.027 0.002 PHE R 265 TYR 0.015 0.002 TYR R 427 ARG 0.013 0.003 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.297 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.0678 time to fit residues: 4.1945 Evaluate side-chains 41 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3083 Z= 0.158 Angle : 0.494 5.690 4279 Z= 0.289 Chirality : 0.045 0.153 562 Planarity : 0.002 0.029 603 Dihedral : 5.141 18.019 567 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 6.25 % Allowed : 27.50 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.38), residues: 557 helix: 2.67 (0.35), residues: 209 sheet: -2.22 (0.83), residues: 45 loop : -2.19 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 491 HIS 0.003 0.001 HIS R 214 PHE 0.011 0.001 PHE R 265 TYR 0.008 0.001 TYR R 427 ARG 0.006 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.333 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.0680 time to fit residues: 4.1414 Evaluate side-chains 41 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 3083 Z= 0.419 Angle : 0.708 9.393 4279 Z= 0.418 Chirality : 0.049 0.152 562 Planarity : 0.004 0.034 603 Dihedral : 6.714 24.871 567 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.18 % Favored : 85.82 % Rotamer: Outliers : 8.75 % Allowed : 27.50 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -1.30 (0.37), residues: 557 helix: 1.81 (0.35), residues: 214 sheet: -2.78 (0.80), residues: 43 loop : -2.77 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 367 HIS 0.011 0.004 HIS R 214 PHE 0.031 0.002 PHE R 265 TYR 0.016 0.003 TYR R 240 ARG 0.018 0.004 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.298 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.0632 time to fit residues: 3.9931 Evaluate side-chains 42 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3083 Z= 0.304 Angle : 0.644 9.497 4279 Z= 0.372 Chirality : 0.047 0.154 562 Planarity : 0.003 0.032 603 Dihedral : 6.382 22.118 567 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 7.50 % Allowed : 28.75 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -1.30 (0.37), residues: 557 helix: 1.88 (0.35), residues: 214 sheet: -2.85 (0.82), residues: 41 loop : -2.83 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 367 HIS 0.005 0.003 HIS R 214 PHE 0.021 0.001 PHE R 265 TYR 0.011 0.002 TYR R 240 ARG 0.011 0.002 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.297 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0605 time to fit residues: 3.8928 Evaluate side-chains 42 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.0040 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 overall best weight: 0.5670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3083 Z= 0.157 Angle : 0.528 9.228 4279 Z= 0.300 Chirality : 0.045 0.145 562 Planarity : 0.002 0.027 603 Dihedral : 5.072 19.209 567 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 6.25 % Allowed : 28.75 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.38), residues: 557 helix: 2.61 (0.35), residues: 209 sheet: -2.97 (0.81), residues: 43 loop : -2.32 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 491 HIS 0.002 0.001 HIS R 214 PHE 0.008 0.001 PHE R 265 TYR 0.013 0.001 TYR R 275 ARG 0.006 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.318 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 42 average time/residue: 0.0697 time to fit residues: 4.5144 Evaluate side-chains 44 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 246 GLN R 278 HIS R 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 3083 Z= 0.562 Angle : 0.841 11.552 4279 Z= 0.492 Chirality : 0.052 0.172 562 Planarity : 0.005 0.037 603 Dihedral : 7.353 29.567 567 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.98 % Favored : 84.02 % Rotamer: Outliers : 8.75 % Allowed : 27.50 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -1.92 (0.35), residues: 557 helix: 1.35 (0.34), residues: 215 sheet: -2.99 (1.96), residues: 10 loop : -3.29 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 367 HIS 0.015 0.005 HIS R 214 PHE 0.041 0.002 PHE R 265 TYR 0.021 0.004 TYR R 240 ARG 0.023 0.005 ARG R 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1114 Ramachandran restraints generated. 557 Oldfield, 0 Emsley, 557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.334 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 40 average time/residue: 0.0663 time to fit residues: 4.1965 Evaluate side-chains 42 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.208494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.205000 restraints weight = 5974.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.202418 restraints weight = 7588.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.201938 restraints weight = 8562.357| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4437 r_free = 0.4437 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3083 Z= 0.250 Angle : 0.625 9.640 4279 Z= 0.359 Chirality : 0.047 0.157 562 Planarity : 0.003 0.030 603 Dihedral : 6.267 21.781 567 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 8.75 % Allowed : 27.50 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -1.48 (0.37), residues: 557 helix: 1.86 (0.35), residues: 214 sheet: -3.27 (1.83), residues: 10 loop : -3.10 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 491 HIS 0.007 0.003 HIS R 429 PHE 0.014 0.001 PHE R 265 TYR 0.012 0.002 TYR R 275 ARG 0.010 0.002 ARG R 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 850.30 seconds wall clock time: 19 minutes 35.65 seconds (1175.65 seconds total)