Starting phenix.real_space_refine on Fri Aug 2 17:39:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/08_2024/8r8k_19002.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/08_2024/8r8k_19002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/08_2024/8r8k_19002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/08_2024/8r8k_19002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/08_2024/8r8k_19002.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/08_2024/8r8k_19002.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2548 2.51 5 N 674 2.21 5 O 766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 337": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "L ASP 1": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4005 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 17, 'TRANS': 262} Chain: "H" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 4.31, per 1000 atoms: 1.08 Number of scatterers: 4005 At special positions: 0 Unit cell: (62.0755, 89.0966, 108.815, 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 17 16.00 O 766 8.00 N 674 7.00 C 2548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 1.43 Conformation dependent library (CDL) restraints added in 732.4 milliseconds 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 10.9% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.531A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.520A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.771A pdb=" N VAL A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 4.529A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.962A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.188A pdb=" N THR H 93 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.125A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 325 removed outlier: 5.740A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.508A pdb=" N TYR A 393 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.848A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.132A pdb=" N TRP H 33 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.460A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 300 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: 1.07 Time building geometry restraints manager: 1.59 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: 1287 1.34 - 1.46: 991 1.46 - 1.58: 1806 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4104 Sorted by residual: bond pdb=" C GLN L 38 " pdb=" N LYS L 39 " ideal model delta sigma weight residual 1.331 1.310 0.021 2.83e-02 1.25e+03 5.55e-01 bond pdb=" CG PRO A 524 " pdb=" CD PRO A 524 " ideal model delta sigma weight residual 1.503 1.480 0.023 3.40e-02 8.65e+02 4.44e-01 bond pdb=" CA PHE H 105 " pdb=" C PHE H 105 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.37e-02 5.33e+03 4.23e-01 bond pdb=" CA ILE A 431 " pdb=" CB ILE A 431 " ideal model delta sigma weight residual 1.540 1.532 0.008 1.23e-02 6.61e+03 4.11e-01 bond pdb=" N SER L 7 " pdb=" CA SER L 7 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.41e-02 5.03e+03 4.01e-01 ... (remaining 4099 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.54: 136 107.54 - 114.14: 2228 114.14 - 120.74: 1613 120.74 - 127.35: 1555 127.35 - 133.95: 37 Bond angle restraints: 5569 Sorted by residual: angle pdb=" C HIS A 516 " pdb=" N ALA A 517 " pdb=" CA ALA A 517 " ideal model delta sigma weight residual 120.86 124.65 -3.79 1.60e+00 3.91e-01 5.60e+00 angle pdb=" N ASN A 484 " pdb=" CA ASN A 484 " pdb=" CB ASN A 484 " ideal model delta sigma weight residual 113.65 110.23 3.42 1.47e+00 4.63e-01 5.42e+00 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 113.65 110.43 3.22 1.47e+00 4.63e-01 4.80e+00 angle pdb=" C PRO A 370 " pdb=" N PHE A 371 " pdb=" CA PHE A 371 " ideal model delta sigma weight residual 121.97 125.24 -3.27 1.73e+00 3.34e-01 3.57e+00 angle pdb=" N PHE A 371 " pdb=" CA PHE A 371 " pdb=" C PHE A 371 " ideal model delta sigma weight residual 110.64 113.40 -2.76 1.48e+00 4.57e-01 3.48e+00 ... (remaining 5564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 2087 14.55 - 29.10: 232 29.10 - 43.64: 68 43.64 - 58.19: 23 58.19 - 72.74: 15 Dihedral angle restraints: 2425 sinusoidal: 947 harmonic: 1478 Sorted by residual: dihedral pdb=" CB CYS A 388 " pdb=" SG CYS A 388 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual 93.00 124.82 -31.82 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 98 " pdb=" CB CYS H 98 " ideal model delta sinusoidal sigma weight residual 93.00 63.87 29.13 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA ASP L 70 " pdb=" CB ASP L 70 " pdb=" CG ASP L 70 " pdb=" OD1 ASP L 70 " ideal model delta sinusoidal sigma weight residual -30.00 -89.37 59.37 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 2422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 367 0.031 - 0.062: 157 0.062 - 0.093: 44 0.093 - 0.124: 31 0.124 - 0.155: 3 Chirality restraints: 602 Sorted by residual: chirality pdb=" CB ILE A 431 " pdb=" CA ILE A 431 " pdb=" CG1 ILE A 431 " pdb=" CG2 ILE A 431 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE A 584 " pdb=" N ILE A 584 " pdb=" C ILE A 584 " pdb=" CB ILE A 584 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 599 not shown) Planarity restraints: 724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 558 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 370 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 371 " -0.008 2.00e-02 2.50e+03 8.43e-03 1.24e+00 pdb=" CG PHE A 371 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 371 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 371 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 371 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 371 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 371 " 0.003 2.00e-02 2.50e+03 ... (remaining 721 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 89 2.70 - 3.25: 3703 3.25 - 3.80: 6041 3.80 - 4.35: 8203 4.35 - 4.90: 13968 Nonbonded interactions: 32004 Sorted by model distance: nonbonded pdb=" O THR A 390 " pdb=" OG1 THR A 520 " model vdw 2.145 3.040 nonbonded pdb=" O SER H 87 " pdb=" OG SER H 87 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP A 395 " pdb=" OH TYR A 420 " model vdw 2.356 3.040 nonbonded pdb=" ND2 ASN A 402 " pdb=" O GLY A 501 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP A 439 " pdb=" OH TYR L 31 " model vdw 2.384 3.040 ... (remaining 31999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.003 0.023 4104 Z= 0.173 Angle : 0.493 6.145 5569 Z= 0.269 Chirality : 0.042 0.155 602 Planarity : 0.004 0.044 724 Dihedral : 15.085 72.737 1464 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.23 % Allowed : 17.73 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.18 (0.38), residues: 509 helix: -3.46 (0.70), residues: 29 sheet: 0.43 (0.42), residues: 173 loop : -0.01 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.018 0.001 PHE A 371 TYR 0.008 0.001 TYR H 82 ARG 0.008 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.463 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1692 time to fit residues: 11.4263 Evaluate side-chains 48 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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: 0.8167 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4104 Z= 0.133 Angle : 0.449 5.046 5569 Z= 0.236 Chirality : 0.042 0.133 602 Planarity : 0.004 0.044 724 Dihedral : 3.548 13.836 562 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.50 % Allowed : 14.55 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.13 (0.38), residues: 509 helix: -3.83 (0.79), residues: 23 sheet: 0.46 (0.42), residues: 172 loop : -0.03 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.006 0.001 PHE A 374 TYR 0.009 0.001 TYR H 82 ARG 0.006 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.467 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1832 time to fit residues: 12.5413 Evaluate side-chains 54 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4104 Z= 0.278 Angle : 0.497 5.083 5569 Z= 0.261 Chirality : 0.044 0.137 602 Planarity : 0.004 0.041 724 Dihedral : 3.864 15.041 560 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.64 % Allowed : 14.09 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.38), residues: 509 helix: -3.92 (0.74), residues: 23 sheet: 0.29 (0.42), residues: 174 loop : -0.08 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.000 0.000 HIS A 516 PHE 0.020 0.001 PHE A 371 TYR 0.009 0.001 TYR A 450 ARG 0.005 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8679 (m-40) cc_final: 0.8368 (m-40) REVERT: A 526 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8063 (ttpp) outliers start: 16 outliers final: 11 residues processed: 61 average time/residue: 0.1894 time to fit residues: 14.3407 Evaluate side-chains 56 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0070 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4104 Z= 0.149 Angle : 0.433 4.568 5569 Z= 0.228 Chirality : 0.042 0.142 602 Planarity : 0.004 0.040 724 Dihedral : 3.595 14.136 560 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.64 % Allowed : 15.00 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.26 (0.38), residues: 509 helix: -3.92 (0.73), residues: 23 sheet: 0.32 (0.42), residues: 172 loop : -0.08 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 502 PHE 0.006 0.001 PHE A 512 TYR 0.008 0.001 TYR A 362 ARG 0.004 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8666 (m-40) cc_final: 0.8350 (m-40) REVERT: A 555 LYS cc_start: 0.5267 (pttm) cc_final: 0.3603 (tmtt) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 0.1867 time to fit residues: 13.1616 Evaluate side-chains 54 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 28 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8220 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4104 Z= 0.180 Angle : 0.440 4.577 5569 Z= 0.232 Chirality : 0.042 0.147 602 Planarity : 0.004 0.039 724 Dihedral : 3.569 14.092 560 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.41 % Allowed : 15.23 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.26 (0.38), residues: 509 helix: -3.94 (0.71), residues: 23 sheet: 0.32 (0.42), residues: 173 loop : -0.07 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.020 0.001 PHE A 371 TYR 0.007 0.001 TYR A 492 ARG 0.003 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8699 (m-40) cc_final: 0.8380 (m-40) REVERT: A 526 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8049 (ttpp) REVERT: A 555 LYS cc_start: 0.5290 (pttm) cc_final: 0.3562 (tmtt) outliers start: 15 outliers final: 13 residues processed: 60 average time/residue: 0.1686 time to fit residues: 12.6984 Evaluate side-chains 58 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4104 Z= 0.175 Angle : 0.439 4.580 5569 Z= 0.230 Chirality : 0.042 0.173 602 Planarity : 0.004 0.039 724 Dihedral : 3.557 13.792 560 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.64 % Allowed : 15.68 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 509 helix: -3.98 (0.69), residues: 23 sheet: 0.31 (0.42), residues: 172 loop : -0.04 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.012 0.001 PHE A 371 TYR 0.007 0.001 TYR A 492 ARG 0.003 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8711 (m-40) cc_final: 0.8401 (m-40) REVERT: A 526 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8056 (ttpp) REVERT: A 555 LYS cc_start: 0.5283 (pttm) cc_final: 0.3571 (tmtt) REVERT: H 78 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7353 (ptmm) outliers start: 16 outliers final: 14 residues processed: 60 average time/residue: 0.1877 time to fit residues: 14.0790 Evaluate side-chains 61 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4104 Z= 0.177 Angle : 0.438 4.583 5569 Z= 0.230 Chirality : 0.042 0.156 602 Planarity : 0.003 0.036 724 Dihedral : 3.543 13.784 560 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.18 % Allowed : 16.36 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 509 helix: -3.85 (0.74), residues: 23 sheet: 0.30 (0.41), residues: 172 loop : -0.04 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.018 0.001 PHE A 371 TYR 0.007 0.001 TYR A 492 ARG 0.005 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8724 (m-40) cc_final: 0.8422 (m-40) REVERT: A 526 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8065 (ttpp) REVERT: A 555 LYS cc_start: 0.5213 (pttm) cc_final: 0.3488 (tmtt) REVERT: H 78 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7349 (ptmm) outliers start: 14 outliers final: 13 residues processed: 57 average time/residue: 0.1817 time to fit residues: 12.9671 Evaluate side-chains 58 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4104 Z= 0.154 Angle : 0.434 4.586 5569 Z= 0.227 Chirality : 0.042 0.136 602 Planarity : 0.003 0.035 724 Dihedral : 3.529 13.608 560 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.86 % Allowed : 15.68 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.22 (0.38), residues: 509 helix: -3.68 (0.78), residues: 23 sheet: 0.28 (0.41), residues: 172 loop : -0.02 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.007 0.001 PHE A 371 TYR 0.006 0.001 TYR H 97 ARG 0.005 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8726 (m-40) cc_final: 0.8424 (m-40) REVERT: A 526 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8079 (ttpp) REVERT: A 555 LYS cc_start: 0.5184 (pttm) cc_final: 0.3482 (tmtt) REVERT: H 78 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7275 (ptmm) outliers start: 17 outliers final: 14 residues processed: 61 average time/residue: 0.1785 time to fit residues: 13.6684 Evaluate side-chains 64 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4104 Z= 0.177 Angle : 0.436 4.582 5569 Z= 0.229 Chirality : 0.042 0.147 602 Planarity : 0.003 0.036 724 Dihedral : 3.502 13.776 560 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.09 % Allowed : 15.00 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.22 (0.37), residues: 509 helix: -3.64 (0.80), residues: 23 sheet: 0.31 (0.41), residues: 172 loop : -0.04 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.016 0.001 PHE A 371 TYR 0.007 0.001 TYR H 97 ARG 0.004 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8758 (m-40) cc_final: 0.8461 (m-40) REVERT: A 526 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8065 (ttpp) REVERT: A 555 LYS cc_start: 0.5277 (pttm) cc_final: 0.3530 (tmtt) REVERT: H 78 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7342 (ptmm) outliers start: 18 outliers final: 15 residues processed: 63 average time/residue: 0.1760 time to fit residues: 13.9350 Evaluate side-chains 60 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4104 Z= 0.216 Angle : 0.451 4.593 5569 Z= 0.237 Chirality : 0.042 0.140 602 Planarity : 0.004 0.035 724 Dihedral : 3.618 14.027 560 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.41 % Allowed : 16.14 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.37), residues: 509 helix: -3.65 (0.80), residues: 23 sheet: 0.23 (0.41), residues: 173 loop : -0.06 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.007 0.001 PHE A 540 TYR 0.008 0.001 TYR H 97 ARG 0.004 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1018 Ramachandran restraints generated. 509 Oldfield, 0 Emsley, 509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8781 (m-40) cc_final: 0.8492 (m-40) REVERT: A 526 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8027 (ttpp) REVERT: A 555 LYS cc_start: 0.5209 (pttm) cc_final: 0.3480 (tmtt) REVERT: H 78 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7383 (ptmm) outliers start: 15 outliers final: 13 residues processed: 59 average time/residue: 0.1656 time to fit residues: 12.4549 Evaluate side-chains 60 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 28 optimal weight: 0.0370 chunk 45 optimal weight: 0.0020 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.1266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.140798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119222 restraints weight = 5846.273| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.47 r_work: 0.3289 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4104 Z= 0.102 Angle : 0.413 4.573 5569 Z= 0.218 Chirality : 0.041 0.128 602 Planarity : 0.003 0.035 724 Dihedral : 3.350 12.808 560 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.50 % Allowed : 17.27 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.17 (0.38), residues: 509 helix: -3.61 (0.79), residues: 23 sheet: 0.35 (0.42), residues: 169 loop : -0.01 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 433 HIS 0.000 0.000 HIS A 516 PHE 0.007 0.001 PHE A 374 TYR 0.005 0.001 TYR A 498 ARG 0.004 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1551.07 seconds wall clock time: 28 minutes 5.29 seconds (1685.29 seconds total)