Starting phenix.real_space_refine on Sat Dec 9 12:02:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/12_2023/7k8d_22728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/12_2023/7k8d_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_22728/12_2023/7k8d_22728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/12_2023/7k8d_22728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/12_2023/7k8d_22728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/12_2023/7k8d_22728.pdb" } resolution = 4.33 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 ------------------------------------------------------------------------------- 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 Anisotropic ADP refinement not supported. Converting 5528 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.80, per 1000 atoms: 0.69 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: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.59 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: 1.60 Time building geometry restraints manager: 2.55 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 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.070 Find NCS groups from input model: 0.160 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4091 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 % Allowed : 9.15 % Favored : 88.98 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 736 HIS 0.007 0.001 HIS A 68 PHE 0.042 0.003 PHE A 12 TYR 0.091 0.005 TYR A 703 ARG 0.003 0.000 ARG A 501 *********************** 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 : 0.594 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: 0.1683 time to fit residues: 35.9498 Evaluate side-chains 114 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0525 time to fit residues: 1.2626 ------------------------------------------------------------------------------- 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: 0.9990 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: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 5639 Z= 0.264 Angle : 0.770 7.616 7672 Z= 0.407 Chirality : 0.047 0.229 917 Planarity : 0.006 0.046 969 Dihedral : 4.480 26.060 770 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.34 % Allowed : 3.39 % Favored : 96.27 % 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: 0.04 (0.30), residues: 721 helix: 0.55 (0.22), residues: 481 sheet: -0.26 (0.98), residues: 21 loop : -0.94 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 737 HIS 0.004 0.001 HIS A 239 PHE 0.024 0.002 PHE A 12 TYR 0.041 0.003 TYR A 703 ARG 0.004 0.001 ARG A 188 *********************** 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 : 0.647 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: 2 outliers final: 1 residues processed: 125 average time/residue: 0.1588 time to fit residues: 26.9080 Evaluate side-chains 107 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0677 time to fit residues: 1.1297 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.4643 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 5639 Z= 0.337 Angle : 0.852 11.769 7672 Z= 0.448 Chirality : 0.048 0.196 917 Planarity : 0.007 0.067 969 Dihedral : 5.040 32.390 770 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.51 % Allowed : 5.42 % Favored : 94.07 % 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: 0.41 (0.32), residues: 721 helix: 0.81 (0.23), residues: 490 sheet: -0.07 (0.84), residues: 21 loop : -0.79 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP A 737 HIS 0.006 0.002 HIS A 615 PHE 0.027 0.003 PHE A 649 TYR 0.033 0.004 TYR A 703 ARG 0.011 0.001 ARG A 514 *********************** 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 121 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.643 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: 3 outliers final: 1 residues processed: 119 average time/residue: 0.1615 time to fit residues: 25.9473 Evaluate side-chains 105 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0505 time to fit residues: 0.8887 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 40.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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: 0.4596 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5639 Z= 0.217 Angle : 0.695 7.147 7672 Z= 0.366 Chirality : 0.044 0.189 917 Planarity : 0.006 0.073 969 Dihedral : 4.640 22.698 770 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 0.60 (0.32), residues: 721 helix: 0.94 (0.23), residues: 500 sheet: -0.44 (0.89), residues: 22 loop : -0.72 (0.49), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 111 HIS 0.007 0.001 HIS A 239 PHE 0.024 0.002 PHE A 649 TYR 0.027 0.002 TYR A 703 ARG 0.004 0.000 ARG A 281 *********************** 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 118 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.615 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: 118 average time/residue: 0.1649 time to fit residues: 25.9101 Evaluate side-chains 110 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9067 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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: 0.4683 moved from start: 0.5636 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= 0.247 Angle : 0.742 7.712 7672 Z= 0.387 Chirality : 0.045 0.226 917 Planarity : 0.006 0.065 969 Dihedral : 4.793 28.118 770 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 1.14 (0.24), residues: 487 sheet: -0.47 (0.92), residues: 22 loop : -0.88 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 111 HIS 0.005 0.002 HIS A 239 PHE 0.020 0.002 PHE A 649 TYR 0.020 0.002 TYR A 703 ARG 0.005 0.001 ARG A 514 *********************** 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 117 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 117 average time/residue: 0.1776 time to fit residues: 27.9844 Evaluate side-chains 103 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8429 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.4710 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5639 Z= 0.230 Angle : 0.730 7.851 7672 Z= 0.379 Chirality : 0.044 0.255 917 Planarity : 0.006 0.070 969 Dihedral : 4.863 28.070 770 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 0.66 (0.32), residues: 721 helix: 1.13 (0.24), residues: 489 sheet: -0.45 (0.93), residues: 22 loop : -1.01 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 111 HIS 0.005 0.002 HIS A 239 PHE 0.038 0.002 PHE A 649 TYR 0.022 0.002 TYR A 703 ARG 0.015 0.001 ARG A 281 *********************** 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 116 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.572 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: 116 average time/residue: 0.1540 time to fit residues: 24.1439 Evaluate side-chains 101 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8638 ------------------------------------------------------------------------------- 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: 6.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 38 optimal weight: 0.1980 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 50.0000 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.4748 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5639 Z= 0.236 Angle : 0.746 7.286 7672 Z= 0.388 Chirality : 0.045 0.205 917 Planarity : 0.006 0.077 969 Dihedral : 4.977 28.326 770 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 0.44 (0.32), residues: 721 helix: 0.89 (0.24), residues: 491 sheet: 0.02 (1.07), residues: 22 loop : -0.99 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 737 HIS 0.006 0.002 HIS A 239 PHE 0.035 0.002 PHE A 311 TYR 0.022 0.002 TYR A 703 ARG 0.008 0.001 ARG A 514 *********************** 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 112 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.651 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: 112 average time/residue: 0.1802 time to fit residues: 26.7298 Evaluate side-chains 99 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8057 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4671 moved from start: 0.6515 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= 0.179 Angle : 0.688 7.070 7672 Z= 0.354 Chirality : 0.043 0.193 917 Planarity : 0.005 0.065 969 Dihedral : 4.687 23.696 770 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 0.64 (0.32), residues: 721 helix: 1.09 (0.24), residues: 488 sheet: 0.20 (1.09), residues: 21 loop : -1.01 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 111 HIS 0.005 0.001 HIS A 239 PHE 0.033 0.002 PHE A 649 TYR 0.021 0.001 TYR A 703 ARG 0.010 0.001 ARG A 281 *********************** 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 116 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.632 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1566 time to fit residues: 24.3753 Evaluate side-chains 96 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8215 ------------------------------------------------------------------------------- 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: 40.0000 chunk 38 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 68 optimal weight: 40.0000 chunk 41 optimal weight: 5.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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: 0.4738 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5639 Z= 0.220 Angle : 0.725 7.150 7672 Z= 0.378 Chirality : 0.044 0.194 917 Planarity : 0.006 0.072 969 Dihedral : 4.878 25.361 770 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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 (0.33), residues: 721 helix: 1.18 (0.24), residues: 484 sheet: 0.39 (1.11), residues: 21 loop : -1.08 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 737 HIS 0.006 0.001 HIS A 239 PHE 0.033 0.002 PHE A 649 TYR 0.019 0.002 TYR A 703 ARG 0.007 0.001 ARG A 281 *********************** 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 111 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.616 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: 111 average time/residue: 0.1682 time to fit residues: 25.2288 Evaluate side-chains 95 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9019 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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: 0.4712 moved from start: 0.7006 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= 0.190 Angle : 0.699 7.322 7672 Z= 0.362 Chirality : 0.044 0.278 917 Planarity : 0.006 0.063 969 Dihedral : 4.778 24.854 770 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.75 (0.32), residues: 721 helix: 1.27 (0.24), residues: 484 sheet: 0.38 (1.11), residues: 21 loop : -1.22 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 737 HIS 0.005 0.001 HIS A 239 PHE 0.035 0.002 PHE A 649 TYR 0.018 0.002 TYR A 703 ARG 0.007 0.001 ARG A 281 ********************** 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 112 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.567 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: 112 average time/residue: 0.1598 time to fit residues: 24.2204 Evaluate side-chains 98 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9127 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 0.0570 chunk 41 optimal weight: 7.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.294652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.266170 restraints weight = 10146.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.269073 restraints weight = 8327.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.272706 restraints weight = 6108.907| |-----------------------------------------------------------------------------| r_work (final): 0.4801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5014 moved from start: 0.7232 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= 0.204 Angle : 0.710 7.179 7672 Z= 0.368 Chirality : 0.044 0.195 917 Planarity : 0.006 0.072 969 Dihedral : 4.838 25.034 770 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.82 (0.33), residues: 721 helix: 1.31 (0.24), residues: 481 sheet: 0.54 (1.13), residues: 21 loop : -1.14 (0.45), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 737 HIS 0.005 0.001 HIS A 239 PHE 0.036 0.002 PHE A 649 TYR 0.019 0.002 TYR A 703 ARG 0.007 0.001 ARG A 281 =============================================================================== Job complete usr+sys time: 1269.45 seconds wall clock time: 23 minutes 52.45 seconds (1432.45 seconds total)