Starting phenix.real_space_refine on Thu Dec 7 20:11:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/12_2023/7fij_31599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/12_2023/7fij_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_31599/12_2023/7fij_31599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/12_2023/7fij_31599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/12_2023/7fij_31599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fij_31599/12_2023/7fij_31599.pdb" } 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 Residue "R ARG 124": "NH1" <-> "NH2" Residue "R ARG 342": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.42, per 1000 atoms: 0.79 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 837.4 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: 0.33 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: 0.90 Time building geometry restraints manager: 1.46 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: 100.92 - 107.53: 68 107.53 - 114.13: 1745 114.13 - 120.74: 1297 120.74 - 127.34: 1159 127.34 - 133.95: 10 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 2.520 nonbonded pdb=" O ILE R 76 " pdb=" N SER R 101 " model vdw 2.398 2.520 nonbonded pdb=" O LEU R 638 " pdb=" N CYS R 644 " model vdw 2.402 2.520 nonbonded pdb=" O ASP R 419 " pdb=" OG1 THR R 422 " model vdw 2.406 2.440 nonbonded pdb=" N ILE R 229 " pdb=" O ILE R 249 " model vdw 2.411 2.520 ... (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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 1.600 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- 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 : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0704 time to fit residues: 3.8246 Evaluate side-chains 35 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4156 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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: 0.5484 moved from start: 0.2889 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= 0.409 Angle : 0.660 8.216 4279 Z= 0.394 Chirality : 0.047 0.145 562 Planarity : 0.004 0.035 603 Dihedral : 5.598 20.778 567 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 5.00 % Allowed : 12.50 % Favored : 82.50 % 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: -0.08 (0.37), residues: 557 helix: 2.59 (0.34), residues: 206 sheet: -1.40 (0.80), residues: 47 loop : -1.85 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 367 HIS 0.009 0.003 HIS R 214 PHE 0.026 0.002 PHE R 265 TYR 0.010 0.002 TYR R 427 ARG 0.017 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 40 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.350 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0678 time to fit residues: 4.0604 Evaluate side-chains 38 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0330 time to fit residues: 0.7208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.5499 moved from start: 0.3635 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= 0.277 Angle : 0.593 9.459 4279 Z= 0.346 Chirality : 0.047 0.171 562 Planarity : 0.003 0.033 603 Dihedral : 5.741 21.253 567 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 5.00 % Allowed : 21.25 % Favored : 73.75 % 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: -0.39 (0.38), residues: 557 helix: 2.34 (0.35), residues: 210 sheet: -1.85 (0.80), residues: 47 loop : -2.05 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 367 HIS 0.008 0.003 HIS R 214 PHE 0.024 0.001 PHE R 265 TYR 0.011 0.001 TYR R 427 ARG 0.013 0.002 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: 4 poor density : 34 time to evaluate : 0.304 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.0832 time to fit residues: 4.6178 Evaluate side-chains 36 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0422 time to fit residues: 0.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.0030 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 overall best weight: 0.9412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3083 Z= 0.185 Angle : 0.499 7.732 4279 Z= 0.290 Chirality : 0.045 0.159 562 Planarity : 0.002 0.029 603 Dihedral : 5.033 18.857 567 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 2.50 % Allowed : 27.50 % 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: -0.24 (0.38), residues: 557 helix: 2.64 (0.35), residues: 209 sheet: -1.88 (0.80), residues: 48 loop : -2.06 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 491 HIS 0.004 0.002 HIS R 214 PHE 0.013 0.001 PHE R 265 TYR 0.010 0.001 TYR R 427 ARG 0.007 0.001 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 37 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.331 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.0671 time to fit residues: 3.8522 Evaluate side-chains 36 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0324 time to fit residues: 0.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.5581 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3083 Z= 0.323 Angle : 0.640 9.278 4279 Z= 0.376 Chirality : 0.047 0.149 562 Planarity : 0.004 0.032 603 Dihedral : 6.396 20.554 567 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 7.50 % Allowed : 25.00 % Favored : 67.50 % 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: -0.95 (0.37), residues: 557 helix: 2.01 (0.35), residues: 214 sheet: -1.97 (0.80), residues: 47 loop : -2.60 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 367 HIS 0.007 0.002 HIS R 214 PHE 0.027 0.002 PHE R 265 TYR 0.016 0.002 TYR R 240 ARG 0.014 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: 6 poor density : 36 time to evaluate : 0.347 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.0737 time to fit residues: 4.5620 Evaluate side-chains 40 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0387 time to fit residues: 0.7354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.0070 chunk 52 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- 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: 0.5547 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3083 Z= 0.251 Angle : 0.577 9.004 4279 Z= 0.336 Chirality : 0.046 0.150 562 Planarity : 0.003 0.031 603 Dihedral : 5.930 19.650 567 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 1.25 % Allowed : 33.75 % 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: -0.90 (0.37), residues: 557 helix: 2.22 (0.35), residues: 214 sheet: -2.31 (0.80), residues: 46 loop : -2.64 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 491 HIS 0.005 0.002 HIS R 214 PHE 0.018 0.001 PHE R 265 TYR 0.013 0.002 TYR R 427 ARG 0.011 0.002 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 39 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.337 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0942 time to fit residues: 5.0525 Evaluate side-chains 37 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 53 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5544 moved from start: 0.4799 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= 0.229 Angle : 0.578 9.031 4279 Z= 0.329 Chirality : 0.046 0.151 562 Planarity : 0.003 0.030 603 Dihedral : 5.780 21.533 567 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 1.25 % Allowed : 33.75 % 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: -0.90 (0.37), residues: 557 helix: 2.49 (0.35), residues: 208 sheet: -2.65 (0.81), residues: 43 loop : -2.72 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 491 HIS 0.004 0.002 HIS R 214 PHE 0.016 0.001 PHE R 265 TYR 0.012 0.002 TYR R 427 ARG 0.009 0.002 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 39 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.354 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.0876 time to fit residues: 4.9203 Evaluate side-chains 39 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0367 time to fit residues: 0.5219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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: 0.5624 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3083 Z= 0.362 Angle : 0.676 9.692 4279 Z= 0.396 Chirality : 0.048 0.154 562 Planarity : 0.004 0.034 603 Dihedral : 6.767 25.857 567 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.08 % Favored : 84.92 % 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: -1.37 (0.37), residues: 557 helix: 1.86 (0.35), residues: 215 sheet: -2.48 (0.90), residues: 36 loop : -2.99 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 367 HIS 0.009 0.003 HIS R 214 PHE 0.025 0.002 PHE R 265 TYR 0.015 0.002 TYR R 427 ARG 0.015 0.004 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 41 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.348 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0936 time to fit residues: 5.1349 Evaluate side-chains 40 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0311 time to fit residues: 0.6259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 0.0570 chunk 44 optimal weight: 0.8980 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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: 0.5524 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3083 Z= 0.188 Angle : 0.568 9.792 4279 Z= 0.320 Chirality : 0.046 0.163 562 Planarity : 0.003 0.028 603 Dihedral : 5.663 20.885 567 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 2.50 % Allowed : 31.25 % 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: -0.95 (0.37), residues: 557 helix: 2.52 (0.35), residues: 208 sheet: -2.88 (0.80), residues: 43 loop : -2.76 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 491 HIS 0.003 0.001 HIS R 214 PHE 0.010 0.001 PHE R 265 TYR 0.016 0.002 TYR R 275 ARG 0.007 0.002 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 fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.344 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.0873 time to fit residues: 5.1549 Evaluate side-chains 41 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0399 time to fit residues: 0.6193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.5582 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3083 Z= 0.277 Angle : 0.629 9.852 4279 Z= 0.358 Chirality : 0.047 0.154 562 Planarity : 0.003 0.032 603 Dihedral : 6.192 23.906 567 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.18 % Favored : 85.82 % Rotamer: Outliers : 2.50 % Allowed : 33.75 % 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: -1.15 (0.37), residues: 557 helix: 2.15 (0.35), residues: 215 sheet: -2.69 (0.87), residues: 38 loop : -2.90 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 491 HIS 0.006 0.002 HIS R 214 PHE 0.017 0.001 PHE R 265 TYR 0.011 0.002 TYR R 427 ARG 0.011 0.003 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 38 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.315 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.0879 time to fit residues: 4.7754 Evaluate side-chains 38 residues out of total 497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0349 time to fit residues: 0.5382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.210466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.204995 restraints weight = 6102.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.204126 restraints weight = 8402.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.203778 restraints weight = 6600.569| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4471 r_free = 0.4471 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4470 r_free = 0.4470 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3083 Z= 0.163 Angle : 0.549 9.966 4279 Z= 0.305 Chirality : 0.045 0.152 562 Planarity : 0.002 0.027 603 Dihedral : 5.234 18.725 567 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 1.25 % Allowed : 35.00 % 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: -0.78 (0.38), residues: 557 helix: 2.56 (0.35), residues: 214 sheet: -2.94 (0.80), residues: 43 loop : -2.67 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 491 HIS 0.002 0.001 HIS R 278 PHE 0.007 0.001 PHE R 265 TYR 0.015 0.002 TYR R 275 ARG 0.005 0.002 ARG R 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 891.75 seconds wall clock time: 16 minutes 40.71 seconds (1000.71 seconds total)