Starting phenix.real_space_refine (version: dev) on Tue Apr 5 04:57:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/04_2022/7k8d_22728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/04_2022/7k8d_22728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/04_2022/7k8d_22728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/04_2022/7k8d_22728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/04_2022/7k8d_22728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/04_2022/7k8d_22728.pdb" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.134 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 63": "NH1" <-> "NH2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 720": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 5529 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5529 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.77, per 1000 atoms: 0.68 Number of scatterers: 5529 At special positions: 0 Unit cell: (76.96, 74.88, 111.28, 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 28 16.00 O 1006 8.00 N 918 7.00 C 3577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.14 Conformation dependent library (CDL) restraints added in 832.6 milliseconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 75.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 4.156A pdb=" N TYR A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.502A pdb=" N LEU A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 62 removed outlier: 3.886A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 101 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 160 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 170 through 205 removed outlier: 3.883A pdb=" N ILE A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 207 through 233 removed outlier: 3.667A pdb=" N ALA A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 241 through 272 removed outlier: 3.705A pdb=" N VAL A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 307 removed outlier: 3.690A pdb=" N THR A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 310 through 332 Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.697A pdb=" N LEU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.805A pdb=" N ALA A 347 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 401 through 416 Proline residue: A 407 - end of helix removed outlier: 3.738A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 428 through 432 removed outlier: 3.726A pdb=" N LEU A 432 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 470 through 483 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.584A pdb=" N LYS A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 583 Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 586 through 612 removed outlier: 4.035A pdb=" N ILE A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.647A pdb=" N MET A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 660 removed outlier: 3.557A pdb=" N ILE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 675 through 695 Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 718 through 732 Proline residue: A 725 - end of helix Processing helix chain 'A' and resid 733 through 737 Processing helix chain 'A' and resid 739 through 748 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73 removed outlier: 3.617A pdb=" N LEU A 73 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 133 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 513 through 518 396 hydrogen bonds defined for protein. 1149 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: 1.62 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1324 1.33 - 1.45: 1034 1.45 - 1.57: 3227 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5639 Sorted by residual: bond pdb=" C ILE A 417 " pdb=" O ILE A 417 " ideal model delta sigma weight residual 1.242 1.224 0.018 8.60e-03 1.35e+04 4.33e+00 bond pdb=" N ALA A 526 " pdb=" CA ALA A 526 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.19e-02 7.06e+03 4.23e+00 bond pdb=" C VAL A 411 " pdb=" O VAL A 411 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.23e-02 6.61e+03 3.57e+00 bond pdb=" CA ASP A 525 " pdb=" C ASP A 525 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.39e+00 bond pdb=" CB MET A 461 " pdb=" CG MET A 461 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.10e+00 ... (remaining 5634 not shown) Histogram of bond angle deviations from ideal: 93.83 - 102.33: 26 102.33 - 110.83: 1875 110.83 - 119.33: 3028 119.33 - 127.83: 2690 127.83 - 136.33: 53 Bond angle restraints: 7672 Sorted by residual: angle pdb=" C LEU A 422 " pdb=" N SER A 423 " pdb=" CA SER A 423 " ideal model delta sigma weight residual 122.81 136.33 -13.52 1.57e+00 4.06e-01 7.42e+01 angle pdb=" N LEU A 422 " pdb=" CA LEU A 422 " pdb=" C LEU A 422 " ideal model delta sigma weight residual 110.23 122.19 -11.96 1.45e+00 4.76e-01 6.80e+01 angle pdb=" C ILE A 417 " pdb=" N PRO A 418 " pdb=" CA PRO A 418 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.01e+00 9.80e-01 6.23e+01 angle pdb=" CA ILE A 417 " pdb=" C ILE A 417 " pdb=" N PRO A 418 " ideal model delta sigma weight residual 120.83 116.10 4.73 6.10e-01 2.69e+00 6.01e+01 angle pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N SER A 423 " ideal model delta sigma weight residual 115.85 108.31 7.54 1.29e+00 6.01e-01 3.41e+01 ... (remaining 7667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3111 17.48 - 34.97: 188 34.97 - 52.45: 61 52.45 - 69.93: 4 69.93 - 87.42: 3 Dihedral angle restraints: 3367 sinusoidal: 1305 harmonic: 2062 Sorted by residual: dihedral pdb=" CA HIS A 239 " pdb=" C HIS A 239 " pdb=" N PHE A 240 " pdb=" CA PHE A 240 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER A 33 " pdb=" C SER A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" N TYR A 703 " pdb=" C TYR A 703 " pdb=" CA TYR A 703 " pdb=" CB TYR A 703 " ideal model delta harmonic sigma weight residual 122.80 131.52 -8.72 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 3364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 808 0.085 - 0.171: 91 0.171 - 0.256: 11 0.256 - 0.341: 6 0.341 - 0.426: 1 Chirality restraints: 917 Sorted by residual: chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CG LEU A 415 " pdb=" CB LEU A 415 " pdb=" CD1 LEU A 415 " pdb=" CD2 LEU A 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA TYR A 703 " pdb=" N TYR A 703 " pdb=" C TYR A 703 " pdb=" CB TYR A 703 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 914 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 703 " -0.041 2.00e-02 2.50e+03 3.70e-02 2.73e+01 pdb=" CG TYR A 703 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TYR A 703 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 703 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 703 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 703 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 703 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 703 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 720 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C ARG A 720 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG A 720 " -0.031 2.00e-02 2.50e+03 pdb=" N MET A 721 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 691 " -0.024 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" C GLY A 691 " 0.083 2.00e-02 2.50e+03 pdb=" O GLY A 691 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA A 692 " -0.028 2.00e-02 2.50e+03 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 699 2.74 - 3.28: 5997 3.28 - 3.82: 8923 3.82 - 4.36: 10012 4.36 - 4.90: 16562 Nonbonded interactions: 42193 Sorted by model distance: nonbonded pdb=" CD1 LEU A 422 " pdb=" O SER A 423 " model vdw 2.205 3.460 nonbonded pdb=" O LEU A 432 " pdb=" NH1 ARG A 439 " model vdw 2.224 2.520 nonbonded pdb=" O PRO A 407 " pdb=" CG2 VAL A 411 " model vdw 2.227 3.460 nonbonded pdb=" O LEU A 414 " pdb=" CD1 ILE A 417 " model vdw 2.243 3.460 nonbonded pdb=" NH1 ARG A 65 " pdb=" OD1 ASN A 504 " model vdw 2.254 2.520 ... (remaining 42188 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3577 2.51 5 N 918 2.21 5 O 1006 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.800 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 18.930 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4024 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 : 0.004 0.053 5639 Z= 0.251 Angle : 1.121 13.520 7672 Z= 0.691 Chirality : 0.061 0.426 917 Planarity : 0.009 0.080 969 Dihedral : 12.529 87.415 2041 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.98 (0.27), residues: 721 helix: -1.95 (0.19), residues: 494 sheet: -1.26 (0.95), residues: 21 loop : -1.56 (0.42), residues: 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 4 residues processed: 165 average time/residue: 0.1605 time to fit residues: 34.6136 Evaluate side-chains 113 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0507 time to fit residues: 1.2463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4312 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 5639 Z= 0.251 Angle : 0.782 7.706 7672 Z= 0.414 Chirality : 0.047 0.218 917 Planarity : 0.006 0.048 969 Dihedral : 4.559 27.724 770 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.30), residues: 721 helix: 0.64 (0.22), residues: 474 sheet: -0.20 (0.98), residues: 21 loop : -1.08 (0.43), residues: 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 125 average time/residue: 0.1454 time to fit residues: 24.5724 Evaluate side-chains 109 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0521 time to fit residues: 0.9437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 0.0030 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 50.0000 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.5998 ------------------------------------------------------------------------------- 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: 0.4454 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 5639 Z= 0.238 Angle : 0.729 8.838 7672 Z= 0.380 Chirality : 0.044 0.197 917 Planarity : 0.006 0.087 969 Dihedral : 4.533 30.908 770 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.76 (0.32), residues: 721 helix: 1.11 (0.23), residues: 487 sheet: 0.13 (0.93), residues: 21 loop : -0.73 (0.47), residues: 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1492 time to fit residues: 24.0387 Evaluate side-chains 103 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 50.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4471 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5639 Z= 0.205 Angle : 0.681 6.570 7672 Z= 0.357 Chirality : 0.044 0.189 917 Planarity : 0.005 0.066 969 Dihedral : 4.528 27.351 770 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.32), residues: 721 helix: 1.10 (0.23), residues: 496 sheet: 0.25 (0.92), residues: 21 loop : -0.71 (0.47), residues: 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.1676 time to fit residues: 27.1321 Evaluate side-chains 98 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0788 time to fit residues: 1.0202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5639 Z= 0.196 Angle : 0.683 6.615 7672 Z= 0.357 Chirality : 0.043 0.183 917 Planarity : 0.005 0.062 969 Dihedral : 4.483 24.075 770 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.32), residues: 721 helix: 1.17 (0.24), residues: 495 sheet: 0.10 (0.90), residues: 21 loop : -0.74 (0.47), residues: 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1442 time to fit residues: 22.2378 Evaluate side-chains 95 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 0.0070 chunk 57 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4598 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5639 Z= 0.216 Angle : 0.721 10.909 7672 Z= 0.374 Chirality : 0.044 0.204 917 Planarity : 0.005 0.068 969 Dihedral : 4.748 30.246 770 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.86 (0.32), residues: 721 helix: 1.23 (0.24), residues: 489 sheet: 0.03 (0.90), residues: 21 loop : -0.84 (0.46), residues: 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1440 time to fit residues: 22.3770 Evaluate side-chains 98 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4581 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5639 Z= 0.199 Angle : 0.700 6.910 7672 Z= 0.363 Chirality : 0.043 0.205 917 Planarity : 0.005 0.067 969 Dihedral : 4.662 25.695 770 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.32), residues: 721 helix: 1.27 (0.24), residues: 487 sheet: -0.08 (0.95), residues: 22 loop : -0.92 (0.46), residues: 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1571 time to fit residues: 24.3871 Evaluate side-chains 98 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 66 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4729 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 5639 Z= 0.274 Angle : 0.805 9.769 7672 Z= 0.421 Chirality : 0.045 0.191 917 Planarity : 0.006 0.070 969 Dihedral : 5.274 30.928 770 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.38 (0.32), residues: 721 helix: 0.97 (0.24), residues: 486 sheet: -0.27 (0.81), residues: 31 loop : -1.30 (0.45), residues: 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1466 time to fit residues: 21.0977 Evaluate side-chains 92 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4759 moved from start: 0.7260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.111 5639 Z= 0.305 Angle : 0.801 7.938 7672 Z= 0.425 Chirality : 0.045 0.197 917 Planarity : 0.008 0.129 969 Dihedral : 5.400 29.179 770 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.32), residues: 721 helix: 0.82 (0.24), residues: 483 sheet: -0.43 (0.77), residues: 29 loop : -1.43 (0.44), residues: 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1589 time to fit residues: 22.6653 Evaluate side-chains 90 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.0670 chunk 47 optimal weight: 30.0000 chunk 71 optimal weight: 0.0570 chunk 66 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4723 moved from start: 0.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 5639 Z= 0.260 Angle : 0.767 7.805 7672 Z= 0.404 Chirality : 0.045 0.197 917 Planarity : 0.007 0.117 969 Dihedral : 5.362 33.551 770 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 (0.32), residues: 721 helix: 0.99 (0.24), residues: 477 sheet: -0.69 (0.79), residues: 29 loop : -1.34 (0.44), residues: 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1502 time to fit residues: 21.9962 Evaluate side-chains 94 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 0.0070 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 162 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.296041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.267553 restraints weight = 11090.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.271053 restraints weight = 7915.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.273303 restraints weight = 6286.438| |-----------------------------------------------------------------------------| r_work (final): 0.4789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4938 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 5639 Z= 0.208 Angle : 0.734 11.702 7672 Z= 0.375 Chirality : 0.044 0.190 917 Planarity : 0.008 0.111 969 Dihedral : 4.973 25.684 770 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.32), residues: 721 helix: 1.34 (0.24), residues: 473 sheet: -0.62 (0.86), residues: 29 loop : -1.27 (0.44), residues: 219 =============================================================================== Job complete usr+sys time: 1172.79 seconds wall clock time: 22 minutes 12.39 seconds (1332.39 seconds total)