Starting phenix.real_space_refine on Mon Jun 24 18:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/06_2024/8r8k_19002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/06_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_19002/06_2024/8r8k_19002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/06_2024/8r8k_19002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/06_2024/8r8k_19002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r8k_19002/06_2024/8r8k_19002.pdb" } 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-5370/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: 4.71, per 1000 atoms: 1.18 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: 1.42 Conformation dependent library (CDL) restraints added in 957.5 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: 0.53 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: 1.28 Time building geometry restraints manager: 1.58 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 2.440 nonbonded pdb=" O SER H 87 " pdb=" OG SER H 87 " model vdw 2.273 2.440 nonbonded pdb=" OD2 ASP A 395 " pdb=" OH TYR A 420 " model vdw 2.356 2.440 nonbonded pdb=" ND2 ASN A 402 " pdb=" O GLY A 501 " model vdw 2.364 2.520 nonbonded pdb=" OD1 ASP A 439 " pdb=" OH TYR L 31 " model vdw 2.384 2.440 ... (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 ========== 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: 4.250 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: 18.650 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.920 Find NCS groups from input model: 0.110 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.760 ------------------------------------------------------------------------------- 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 : 0.458 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1633 time to fit residues: 11.0011 Evaluate side-chains 48 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4104 Z= 0.358 Angle : 0.551 5.715 5569 Z= 0.290 Chirality : 0.045 0.141 602 Planarity : 0.004 0.044 724 Dihedral : 4.166 16.015 562 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.64 % Allowed : 16.59 % Favored : 79.77 % 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: -0.44 (0.37), residues: 509 helix: -3.92 (0.81), residues: 23 sheet: 0.24 (0.42), residues: 174 loop : -0.25 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.001 0.000 HIS A 516 PHE 0.012 0.002 PHE A 540 TYR 0.012 0.001 TYR H 82 ARG 0.005 0.001 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 62 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8766 (m-40) cc_final: 0.8459 (m-40) REVERT: A 555 LYS cc_start: 0.4923 (pttm) cc_final: 0.3171 (tmtt) outliers start: 16 outliers final: 13 residues processed: 57 average time/residue: 0.1956 time to fit residues: 13.6739 Evaluate side-chains 56 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 447 ASN 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 86 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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: 0.8213 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4104 Z= 0.151 Angle : 0.444 4.567 5569 Z= 0.233 Chirality : 0.042 0.138 602 Planarity : 0.004 0.042 724 Dihedral : 3.656 14.786 560 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.73 % Allowed : 16.82 % 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: -0.33 (0.38), residues: 509 helix: -4.02 (0.72), residues: 23 sheet: 0.29 (0.42), residues: 174 loop : -0.14 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 433 HIS 0.000 0.000 HIS A 502 PHE 0.007 0.001 PHE A 512 TYR 0.005 0.001 TYR H 97 ARG 0.005 0.000 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 64 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8737 (m-40) cc_final: 0.8415 (m-40) REVERT: A 555 LYS cc_start: 0.5028 (pttm) cc_final: 0.3267 (tmtt) outliers start: 12 outliers final: 9 residues processed: 58 average time/residue: 0.1905 time to fit residues: 13.6407 Evaluate side-chains 58 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1351 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= 0.276 Angle : 0.483 4.567 5569 Z= 0.255 Chirality : 0.043 0.144 602 Planarity : 0.004 0.039 724 Dihedral : 3.877 15.355 560 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.00 % Allowed : 15.23 % Favored : 79.77 % 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: -0.46 (0.38), residues: 509 helix: -4.02 (0.75), residues: 23 sheet: 0.20 (0.40), residues: 184 loop : -0.24 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS A 516 PHE 0.018 0.001 PHE A 371 TYR 0.009 0.001 TYR A 450 ARG 0.003 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 72 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 50 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8837 (m-40) cc_final: 0.8538 (m-40) REVERT: A 555 LYS cc_start: 0.4995 (pttm) cc_final: 0.3125 (tmtt) outliers start: 22 outliers final: 17 residues processed: 64 average time/residue: 0.1765 time to fit residues: 14.1808 Evaluate side-chains 64 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 520 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 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER 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: 0.9980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4104 Z= 0.176 Angle : 0.445 4.568 5569 Z= 0.234 Chirality : 0.042 0.170 602 Planarity : 0.004 0.037 724 Dihedral : 3.701 14.832 560 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.32 % Allowed : 15.68 % Favored : 80.00 % 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: -0.43 (0.38), residues: 509 helix: -4.02 (0.73), residues: 23 sheet: 0.21 (0.40), residues: 184 loop : -0.22 (0.36), residues: 302 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 0.011 0.001 PHE A 371 TYR 0.007 0.001 TYR A 362 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 73 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8827 (m-40) cc_final: 0.8532 (m-40) REVERT: A 555 LYS cc_start: 0.4871 (pttm) cc_final: 0.3010 (tmtt) outliers start: 19 outliers final: 18 residues processed: 66 average time/residue: 0.1854 time to fit residues: 15.0495 Evaluate side-chains 67 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 447 ASN 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 21 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 0.0030 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- 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: 0.8239 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4104 Z= 0.210 Angle : 0.451 4.587 5569 Z= 0.237 Chirality : 0.043 0.151 602 Planarity : 0.004 0.036 724 Dihedral : 3.699 14.821 560 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.23 % Allowed : 15.23 % Favored : 79.55 % 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: -0.46 (0.38), residues: 509 helix: -3.97 (0.75), residues: 23 sheet: 0.14 (0.40), residues: 184 loop : -0.21 (0.36), residues: 302 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 0.020 0.001 PHE A 371 TYR 0.008 0.001 TYR A 362 ARG 0.003 0.000 ARG H 19 *********************** 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 76 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 53 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8824 (m-40) cc_final: 0.8534 (m-40) REVERT: A 555 LYS cc_start: 0.4840 (pttm) cc_final: 0.2903 (tmtt) outliers start: 23 outliers final: 21 residues processed: 69 average time/residue: 0.1668 time to fit residues: 14.4679 Evaluate side-chains 72 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 442 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 553 ASN 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 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4104 Z= 0.204 Angle : 0.446 4.587 5569 Z= 0.234 Chirality : 0.042 0.146 602 Planarity : 0.004 0.036 724 Dihedral : 3.671 14.666 560 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.00 % Allowed : 16.82 % Favored : 78.18 % 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: -0.44 (0.38), residues: 509 helix: -3.83 (0.77), residues: 23 sheet: 0.15 (0.40), residues: 184 loop : -0.19 (0.36), residues: 302 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 0.008 0.001 PHE A 371 TYR 0.006 0.001 TYR A 492 ARG 0.003 0.000 ARG H 19 *********************** 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 77 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 55 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8807 (m-40) cc_final: 0.8522 (m-40) REVERT: A 555 LYS cc_start: 0.4629 (pttm) cc_final: 0.2643 (tmtt) REVERT: H 78 LYS cc_start: 0.7615 (ptmm) cc_final: 0.7404 (pttm) outliers start: 22 outliers final: 21 residues processed: 70 average time/residue: 0.1862 time to fit residues: 15.8901 Evaluate side-chains 71 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 442 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 553 ASN 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 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8230 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4104 Z= 0.192 Angle : 0.442 4.597 5569 Z= 0.232 Chirality : 0.042 0.145 602 Planarity : 0.004 0.044 724 Dihedral : 3.646 14.441 560 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.77 % Allowed : 17.05 % Favored : 78.18 % 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: -0.40 (0.38), residues: 509 helix: -3.81 (0.76), residues: 23 sheet: 0.17 (0.40), residues: 184 loop : -0.16 (0.36), residues: 302 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 0.008 0.001 PHE A 371 TYR 0.009 0.001 TYR A 362 ARG 0.009 0.000 ARG H 19 *********************** 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 73 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8812 (m-40) cc_final: 0.8530 (m-40) REVERT: A 555 LYS cc_start: 0.4603 (pttm) cc_final: 0.2604 (tmtt) outliers start: 21 outliers final: 20 residues processed: 66 average time/residue: 0.1779 time to fit residues: 14.7439 Evaluate side-chains 71 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 553 ASN 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 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 77 SER 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: 0.3980 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.8213 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 0.028 4104 Z= 0.161 Angle : 0.433 4.597 5569 Z= 0.227 Chirality : 0.042 0.212 602 Planarity : 0.004 0.041 724 Dihedral : 3.580 14.147 560 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.00 % Allowed : 16.82 % Favored : 78.18 % 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: -0.34 (0.38), residues: 509 helix: -3.76 (0.77), residues: 23 sheet: 0.20 (0.41), residues: 174 loop : -0.11 (0.36), residues: 312 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 0.006 0.001 PHE A 540 TYR 0.006 0.001 TYR H 97 ARG 0.009 0.000 ARG H 19 *********************** 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 75 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 457 ASN cc_start: 0.8789 (m-40) cc_final: 0.8494 (m-40) REVERT: A 555 LYS cc_start: 0.4582 (pttm) cc_final: 0.2594 (tmtt) REVERT: H 120 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7817 (pm20) outliers start: 22 outliers final: 21 residues processed: 67 average time/residue: 0.1839 time to fit residues: 15.2381 Evaluate side-chains 74 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 553 ASN 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 81 LEU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU 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: 2.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 overall best weight: 0.3286 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4104 Z= 0.117 Angle : 0.416 4.603 5569 Z= 0.217 Chirality : 0.041 0.136 602 Planarity : 0.003 0.035 724 Dihedral : 3.353 13.240 560 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.86 % Allowed : 18.18 % Favored : 77.95 % 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: -0.25 (0.38), residues: 509 helix: -3.63 (0.82), residues: 23 sheet: 0.26 (0.41), residues: 173 loop : -0.05 (0.36), 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 502 PHE 0.009 0.001 PHE A 371 TYR 0.005 0.001 TYR A 492 ARG 0.005 0.000 ARG H 19 ********************** 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 72 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.8378 (mm110) cc_final: 0.7494 (mp10) REVERT: A 457 ASN cc_start: 0.8788 (m-40) cc_final: 0.8491 (m-40) outliers start: 17 outliers final: 16 residues processed: 66 average time/residue: 0.1823 time to fit residues: 15.1040 Evaluate side-chains 68 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 ASN 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 81 LEU Chi-restraints excluded: chain H residue 86 ASN 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 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: 0.6980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 GLN ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117212 restraints weight = 5847.186| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.44 r_work: 0.3261 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1735 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= 0.143 Angle : 0.421 4.621 5569 Z= 0.220 Chirality : 0.042 0.133 602 Planarity : 0.004 0.035 724 Dihedral : 3.361 13.403 560 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.32 % Allowed : 18.41 % Favored : 77.27 % 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: -0.22 (0.38), residues: 509 helix: -3.59 (0.84), residues: 23 sheet: 0.29 (0.41), residues: 173 loop : -0.03 (0.36), residues: 313 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 0.006 0.001 PHE A 374 TYR 0.006 0.001 TYR A 492 ARG 0.004 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1574.34 seconds wall clock time: 28 minutes 35.68 seconds (1715.68 seconds total)