Starting phenix.real_space_refine on Tue Feb 11 03:57:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fij_31599/02_2025/7fij_31599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fij_31599/02_2025/7fij_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/cci-nas-00/data/ceres_data/7fij_31599/02_2025/7fij_31599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fij_31599/02_2025/7fij_31599.map" model { file = "/net/cci-nas-00/data/ceres_data/7fij_31599/02_2025/7fij_31599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fij_31599/02_2025/7fij_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-5592/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: 2.50, per 1000 atoms: 0.82 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: 0.85 Conformation dependent library (CDL) restraints added in 467.1 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: 0.31 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: 0.85 Time building geometry restraints manager: 0.98 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: 0.440 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.240 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0718 time to fit residues: 3.9780 Evaluate side-chains 35 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.216278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.209761 restraints weight = 6258.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.209529 restraints weight = 8040.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.209997 restraints weight = 6445.624| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4542 r_free = 0.4542 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4542 r_free = 0.4542 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5236 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 : 5.41 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 to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.329 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0667 time to fit residues: 4.0860 Evaluate side-chains 39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 5 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.206136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.201451 restraints weight = 5914.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.200924 restraints weight = 8656.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.201035 restraints weight = 8196.655| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4446 r_free = 0.4446 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 3083 Z= 0.538 Angle : 0.840 11.202 4279 Z= 0.497 Chirality : 0.052 0.181 562 Planarity : 0.005 0.041 603 Dihedral : 7.512 26.648 567 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 8.75 % Allowed : 21.25 % Favored : 70.00 % 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: -1.38 (0.36), residues: 557 helix: 1.40 (0.34), residues: 208 sheet: -2.32 (0.74), residues: 48 loop : -2.51 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 367 HIS 0.018 0.006 HIS R 214 PHE 0.042 0.003 PHE R 265 TYR 0.019 0.003 TYR R 240 ARG 0.023 0.004 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 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.315 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 0.0656 time to fit residues: 4.0754 Evaluate side-chains 40 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 162 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.210478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.203626 restraints weight = 6174.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.202358 restraints weight = 9656.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.203150 restraints weight = 8767.861| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4469 r_free = 0.4469 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4469 r_free = 0.4469 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3083 Z= 0.217 Angle : 0.553 8.159 4279 Z= 0.323 Chirality : 0.045 0.142 562 Planarity : 0.003 0.032 603 Dihedral : 5.828 20.200 567 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.75 % Allowed : 25.00 % Favored : 71.25 % 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: -0.74 (0.37), residues: 557 helix: 2.32 (0.36), residues: 204 sheet: -2.20 (0.79), residues: 47 loop : -2.35 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 491 HIS 0.006 0.002 HIS R 214 PHE 0.015 0.001 PHE R 265 TYR 0.011 0.002 TYR R 427 ARG 0.009 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 39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.317 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0800 time to fit residues: 4.8175 Evaluate side-chains 39 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU 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 5 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 0.0040 chunk 3 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.209262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.204992 restraints weight = 6116.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.204627 restraints weight = 8825.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.204546 restraints weight = 8464.198| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4487 r_free = 0.4487 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4487 r_free = 0.4487 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.4469 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= 0.255 Angle : 0.588 8.827 4279 Z= 0.342 Chirality : 0.046 0.159 562 Planarity : 0.003 0.032 603 Dihedral : 5.962 20.506 567 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 7.50 % Allowed : 26.25 % 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: -0.91 (0.38), residues: 557 helix: 2.13 (0.36), residues: 214 sheet: -2.24 (0.82), residues: 45 loop : -2.59 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 491 HIS 0.005 0.002 HIS R 214 PHE 0.022 0.001 PHE R 265 TYR 0.013 0.002 TYR R 427 ARG 0.011 0.002 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 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.291 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 41 average time/residue: 0.0692 time to fit residues: 4.3594 Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.204474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.200022 restraints weight = 6076.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.199477 restraints weight = 9346.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.199345 restraints weight = 8235.435| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4421 r_free = 0.4421 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 3083 Z= 0.545 Angle : 0.847 12.855 4279 Z= 0.497 Chirality : 0.052 0.171 562 Planarity : 0.005 0.041 603 Dihedral : 7.839 30.016 567 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.08 % Favored : 84.92 % 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 : 0.19 % 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: -1.90 (0.36), residues: 557 helix: 1.26 (0.34), residues: 207 sheet: -3.06 (0.76), residues: 42 loop : -2.98 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 367 HIS 0.012 0.005 HIS R 214 PHE 0.051 0.002 PHE R 265 TYR 0.026 0.004 TYR R 240 ARG 0.024 0.005 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 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.293 Fit side-chains REVERT: R 359 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.6064 (m-80) outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.0663 time to fit residues: 4.1148 Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 359 TYR Chi-restraints excluded: chain R residue 422 THR Chi-restraints excluded: chain R residue 429 HIS Chi-restraints excluded: chain R residue 468 ILE 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 38 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 = 0.4567 r_free = 0.4567 target = 0.211960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4502 r_free = 0.4502 target = 0.206424 restraints weight = 6247.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.205398 restraints weight = 9210.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.205919 restraints weight = 8488.987| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3083 Z= 0.154 Angle : 0.519 7.005 4279 Z= 0.300 Chirality : 0.045 0.152 562 Planarity : 0.002 0.028 603 Dihedral : 5.226 17.457 567 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 5.00 % Allowed : 31.25 % 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: -0.68 (0.38), residues: 557 helix: 2.59 (0.35), residues: 205 sheet: -2.26 (0.96), residues: 33 loop : -2.52 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 491 HIS 0.001 0.001 HIS R 214 PHE 0.005 0.001 PHE R 265 TYR 0.006 0.001 TYR R 427 ARG 0.005 0.001 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 44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.315 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.0912 time to fit residues: 5.3713 Evaluate side-chains 43 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 429 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4576 r_free = 0.4576 target = 0.212694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.206966 restraints weight = 6191.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.206302 restraints weight = 9362.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.206838 restraints weight = 8129.124| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.4543 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= 0.141 Angle : 0.490 7.550 4279 Z= 0.280 Chirality : 0.044 0.149 562 Planarity : 0.002 0.028 603 Dihedral : 4.615 17.331 567 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % 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: -0.28 (0.39), residues: 557 helix: 2.88 (0.35), residues: 207 sheet: -2.78 (0.80), residues: 43 loop : -2.14 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 491 HIS 0.002 0.001 HIS R 429 PHE 0.009 0.001 PHE R 194 TYR 0.010 0.001 TYR R 275 ARG 0.004 0.001 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 46 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.317 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.0900 time to fit residues: 5.4786 Evaluate side-chains 44 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 243 GLU 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 15 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.206571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.202884 restraints weight = 6028.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.198513 restraints weight = 8218.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.198775 restraints weight = 7954.876| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5615 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 3083 Z= 0.421 Angle : 0.729 10.583 4279 Z= 0.424 Chirality : 0.049 0.164 562 Planarity : 0.004 0.035 603 Dihedral : 6.622 24.484 567 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 7.50 % Allowed : 27.50 % 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: -1.32 (0.37), residues: 557 helix: 1.81 (0.35), residues: 215 sheet: -2.65 (0.81), residues: 40 loop : -2.84 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 367 HIS 0.011 0.004 HIS R 214 PHE 0.027 0.002 PHE R 265 TYR 0.019 0.003 TYR R 240 ARG 0.018 0.004 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 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.402 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.0711 time to fit residues: 4.4637 Evaluate side-chains 40 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 243 GLU 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 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.209925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.206379 restraints weight = 6115.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.202575 restraints weight = 7918.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.202673 restraints weight = 7772.527| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5497 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3083 Z= 0.209 Angle : 0.569 7.716 4279 Z= 0.328 Chirality : 0.046 0.152 562 Planarity : 0.003 0.029 603 Dihedral : 5.688 19.416 567 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % 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: -0.91 (0.38), residues: 557 helix: 2.24 (0.35), residues: 214 sheet: -2.49 (0.86), residues: 40 loop : -2.65 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 491 HIS 0.003 0.002 HIS R 214 PHE 0.011 0.001 PHE R 265 TYR 0.009 0.002 TYR R 240 ARG 0.008 0.002 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 to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.308 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0696 time to fit residues: 4.3830 Evaluate side-chains 42 residues out of total 497 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 243 GLU 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 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.4515 r_free = 0.4515 target = 0.207366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.203871 restraints weight = 6023.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.199658 restraints weight = 7583.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.199807 restraints weight = 6959.964| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.5513 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= 0.328 Angle : 0.663 9.144 4279 Z= 0.382 Chirality : 0.048 0.156 562 Planarity : 0.003 0.032 603 Dihedral : 6.371 23.071 567 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 6.25 % Allowed : 30.00 % 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: -1.32 (0.38), residues: 557 helix: 1.92 (0.35), residues: 217 sheet: -2.69 (0.87), residues: 40 loop : -2.97 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 367 HIS 0.008 0.003 HIS R 214 PHE 0.018 0.001 PHE R 265 TYR 0.016 0.002 TYR R 240 ARG 0.013 0.002 ARG R 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1214.02 seconds wall clock time: 22 minutes 12.40 seconds (1332.40 seconds total)