Starting phenix.real_space_refine on Fri Mar 15 07:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/03_2024/7k8d_22728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/03_2024/7k8d_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_22728/03_2024/7k8d_22728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/03_2024/7k8d_22728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/03_2024/7k8d_22728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8d_22728/03_2024/7k8d_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.57, per 1000 atoms: 0.65 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: 2.08 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: 0.53 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: 1.75 Time building geometry restraints manager: 2.29 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: 0.050 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.110 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- 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. REVERT: A 20 MET cc_start: 0.5777 (tmm) cc_final: 0.4769 (tpp) REVERT: A 79 LYS cc_start: 0.7398 (mmpt) cc_final: 0.7192 (mmpt) REVERT: A 307 PHE cc_start: 0.4082 (m-10) cc_final: 0.3830 (m-80) REVERT: A 325 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7492 (pp) REVERT: A 414 LEU cc_start: 0.0394 (OUTLIER) cc_final: -0.1126 (mp) REVERT: A 555 ASP cc_start: 0.7868 (m-30) cc_final: 0.7652 (m-30) REVERT: A 559 SER cc_start: 0.8509 (m) cc_final: 0.8097 (p) REVERT: A 580 PHE cc_start: 0.6584 (t80) cc_final: 0.6160 (t80) REVERT: A 640 TRP cc_start: 0.6175 (t-100) cc_final: 0.5698 (t-100) REVERT: A 668 ILE cc_start: 0.4527 (tp) cc_final: 0.4168 (mm) outliers start: 11 outliers final: 4 residues processed: 165 average time/residue: 0.1594 time to fit residues: 34.2539 Evaluate side-chains 117 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 8.9990 chunk 30 optimal weight: 0.0030 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 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: 3.7998 ------------------------------------------------------------------------------- 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: 0.4340 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5639 Z= 0.250 Angle : 0.764 7.640 7672 Z= 0.404 Chirality : 0.046 0.210 917 Planarity : 0.006 0.047 969 Dihedral : 4.487 26.054 770 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.64 % Favored : 97.23 % Rotamer: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.61 % 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: 0.03 (0.30), residues: 721 helix: 0.56 (0.22), residues: 476 sheet: -0.28 (0.98), residues: 21 loop : -0.96 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 737 HIS 0.006 0.001 HIS A 239 PHE 0.029 0.002 PHE A 611 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 125 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 20 MET cc_start: 0.6036 (tmm) cc_final: 0.5607 (tmm) REVERT: A 131 ARG cc_start: 0.4230 (ttt180) cc_final: 0.3732 (ttt180) REVERT: A 171 LEU cc_start: 0.8136 (mp) cc_final: 0.7932 (mp) REVERT: A 284 MET cc_start: 0.2980 (ppp) cc_final: 0.2721 (ppp) REVERT: A 307 PHE cc_start: 0.5590 (m-80) cc_final: 0.5251 (m-80) REVERT: A 412 MET cc_start: 0.3180 (ptt) cc_final: 0.2771 (ptt) REVERT: A 477 MET cc_start: 0.4161 (mtp) cc_final: 0.3876 (mtp) REVERT: A 555 ASP cc_start: 0.8144 (m-30) cc_final: 0.7914 (m-30) REVERT: A 580 PHE cc_start: 0.6852 (t80) cc_final: 0.6278 (t80) REVERT: A 640 TRP cc_start: 0.6588 (t-100) cc_final: 0.6216 (t-100) REVERT: A 649 PHE cc_start: 0.6803 (m-10) cc_final: 0.6391 (m-80) REVERT: A 701 MET cc_start: 0.9250 (tpp) cc_final: 0.8838 (tpp) REVERT: A 704 LEU cc_start: 0.8230 (mt) cc_final: 0.8018 (mt) REVERT: A 715 ASP cc_start: 0.7191 (m-30) cc_final: 0.6928 (m-30) REVERT: A 751 LEU cc_start: 0.8513 (pp) cc_final: 0.7869 (tp) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1454 time to fit residues: 24.3055 Evaluate side-chains 108 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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: 0.4526 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5639 Z= 0.243 Angle : 0.743 7.339 7672 Z= 0.386 Chirality : 0.045 0.184 917 Planarity : 0.006 0.064 969 Dihedral : 4.515 26.751 770 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % 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: 0.68 (0.32), residues: 721 helix: 1.04 (0.23), residues: 486 sheet: 0.10 (0.84), residues: 21 loop : -0.75 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 737 HIS 0.007 0.002 HIS A 239 PHE 0.025 0.002 PHE A 265 TYR 0.028 0.002 TYR A 703 ARG 0.006 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 120 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.635 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 131 ARG cc_start: 0.4500 (ttt180) cc_final: 0.3851 (ttt180) REVERT: A 171 LEU cc_start: 0.8089 (mp) cc_final: 0.7886 (mp) REVERT: A 555 ASP cc_start: 0.8407 (m-30) cc_final: 0.8205 (m-30) REVERT: A 563 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8670 (mmmt) REVERT: A 580 PHE cc_start: 0.7334 (t80) cc_final: 0.6723 (t80) REVERT: A 640 TRP cc_start: 0.6679 (t-100) cc_final: 0.6273 (t-100) REVERT: A 649 PHE cc_start: 0.6926 (m-10) cc_final: 0.6566 (m-80) REVERT: A 700 MET cc_start: 0.6963 (tmm) cc_final: 0.6683 (tmm) REVERT: A 715 ASP cc_start: 0.7246 (m-30) cc_final: 0.6940 (m-30) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1597 time to fit residues: 25.2937 Evaluate side-chains 106 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 20.0000 chunk 33 optimal weight: 40.0000 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 440 GLN ** 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: 0.4714 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5639 Z= 0.319 Angle : 0.818 9.145 7672 Z= 0.433 Chirality : 0.047 0.204 917 Planarity : 0.006 0.061 969 Dihedral : 5.158 33.211 770 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % 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: 0.88 (0.23), residues: 486 sheet: -0.54 (0.79), residues: 21 loop : -0.91 (0.46), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 111 HIS 0.009 0.002 HIS A 540 PHE 0.036 0.003 PHE A 311 TYR 0.034 0.003 TYR A 703 ARG 0.009 0.001 ARG A 400 *********************** 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 119 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.516 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 171 LEU cc_start: 0.8192 (mp) cc_final: 0.7958 (mp) REVERT: A 412 MET cc_start: 0.4479 (ptm) cc_final: 0.4238 (ptt) REVERT: A 563 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8665 (mmmt) REVERT: A 580 PHE cc_start: 0.7408 (t80) cc_final: 0.6737 (t80) REVERT: A 640 TRP cc_start: 0.6804 (t-100) cc_final: 0.6337 (t-100) REVERT: A 649 PHE cc_start: 0.7279 (m-10) cc_final: 0.6993 (m-80) REVERT: A 751 LEU cc_start: 0.8392 (pp) cc_final: 0.7929 (tp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1592 time to fit residues: 25.7861 Evaluate side-chains 98 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** 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: 0.4653 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5639 Z= 0.216 Angle : 0.703 7.303 7672 Z= 0.368 Chirality : 0.044 0.192 917 Planarity : 0.006 0.070 969 Dihedral : 4.824 29.507 770 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 1.12 (0.24), residues: 487 sheet: -0.79 (0.80), residues: 21 loop : -1.07 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 111 HIS 0.005 0.002 HIS A 132 PHE 0.017 0.002 PHE A 12 TYR 0.030 0.002 TYR A 703 ARG 0.010 0.001 ARG A 281 *********************** 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 114 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.529 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. REVERT: A 1 MET cc_start: 0.8249 (tmm) cc_final: 0.7747 (tmm) REVERT: A 146 GLU cc_start: 0.8918 (mp0) cc_final: 0.8717 (mp0) REVERT: A 315 ILE cc_start: 0.8274 (mm) cc_final: 0.8055 (mm) REVERT: A 398 MET cc_start: 0.1936 (tpt) cc_final: 0.1667 (tpp) REVERT: A 463 ARG cc_start: 0.7013 (ptp-110) cc_final: 0.6806 (mtm-85) REVERT: A 563 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8731 (mmmt) REVERT: A 579 MET cc_start: 0.7920 (mmt) cc_final: 0.7708 (mmm) REVERT: A 580 PHE cc_start: 0.7502 (t80) cc_final: 0.7249 (t80) REVERT: A 640 TRP cc_start: 0.6878 (t-100) cc_final: 0.6317 (t-100) REVERT: A 649 PHE cc_start: 0.7203 (m-10) cc_final: 0.6921 (m-80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1537 time to fit residues: 23.4490 Evaluate side-chains 100 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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: 7.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.4681 moved from start: 0.6126 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= 0.199 Angle : 0.705 8.238 7672 Z= 0.361 Chirality : 0.043 0.187 917 Planarity : 0.005 0.070 969 Dihedral : 4.714 26.600 770 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 1.19 (0.24), residues: 488 sheet: -0.66 (0.85), residues: 21 loop : -1.04 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 111 HIS 0.006 0.002 HIS A 239 PHE 0.017 0.002 PHE A 12 TYR 0.027 0.002 TYR A 703 ARG 0.005 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 118 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.609 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. REVERT: A 1 MET cc_start: 0.8065 (tmm) cc_final: 0.7623 (tmm) REVERT: A 477 MET cc_start: 0.3439 (mtp) cc_final: 0.3164 (mtt) REVERT: A 563 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8731 (mmmt) REVERT: A 566 LEU cc_start: 0.8417 (mt) cc_final: 0.8079 (mp) REVERT: A 640 TRP cc_start: 0.6904 (t-100) cc_final: 0.6372 (t-100) REVERT: A 649 PHE cc_start: 0.7260 (m-10) cc_final: 0.7050 (m-80) REVERT: A 751 LEU cc_start: 0.8389 (pp) cc_final: 0.7764 (tp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1573 time to fit residues: 24.7479 Evaluate side-chains 104 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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: 0.4660 moved from start: 0.6337 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= 0.190 Angle : 0.693 6.876 7672 Z= 0.353 Chirality : 0.043 0.197 917 Planarity : 0.006 0.075 969 Dihedral : 4.720 25.455 770 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 0.69 (0.33), residues: 721 helix: 1.17 (0.24), residues: 489 sheet: -0.88 (0.79), residues: 21 loop : -0.97 (0.46), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 111 HIS 0.006 0.001 HIS A 239 PHE 0.016 0.002 PHE A 311 TYR 0.025 0.002 TYR A 703 ARG 0.014 0.001 ARG A 281 *********************** 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 : 0.579 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. REVERT: A 1 MET cc_start: 0.8144 (tmm) cc_final: 0.7713 (tmm) REVERT: A 125 MET cc_start: 0.5909 (tmm) cc_final: 0.5549 (tmm) REVERT: A 265 PHE cc_start: 0.4787 (t80) cc_final: 0.4439 (t80) REVERT: A 563 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8713 (mmmt) REVERT: A 566 LEU cc_start: 0.8405 (mt) cc_final: 0.8072 (mp) REVERT: A 640 TRP cc_start: 0.6853 (t-100) cc_final: 0.6348 (t-100) REVERT: A 751 LEU cc_start: 0.8375 (pp) cc_final: 0.7880 (tp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1391 time to fit residues: 21.8475 Evaluate side-chains 101 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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: 20.0000 chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4786 moved from start: 0.7009 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= 0.263 Angle : 0.776 8.097 7672 Z= 0.403 Chirality : 0.045 0.194 917 Planarity : 0.006 0.073 969 Dihedral : 5.153 31.765 770 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 0.28 (0.32), residues: 721 helix: 0.93 (0.24), residues: 489 sheet: -0.85 (0.69), residues: 31 loop : -1.39 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 737 HIS 0.009 0.002 HIS A 132 PHE 0.032 0.002 PHE A 649 TYR 0.029 0.002 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 112 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 2 PHE cc_start: 0.6288 (m-80) cc_final: 0.5776 (m-80) REVERT: A 20 MET cc_start: 0.6847 (tmm) cc_final: 0.6299 (tpt) REVERT: A 130 LEU cc_start: 0.7962 (mp) cc_final: 0.7248 (tp) REVERT: A 146 GLU cc_start: 0.8849 (mp0) cc_final: 0.8632 (mp0) REVERT: A 265 PHE cc_start: 0.4469 (t80) cc_final: 0.4087 (t80) REVERT: A 555 ASP cc_start: 0.8433 (m-30) cc_final: 0.8162 (m-30) REVERT: A 563 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8622 (mmmt) REVERT: A 566 LEU cc_start: 0.8402 (mt) cc_final: 0.8124 (mt) REVERT: A 640 TRP cc_start: 0.7045 (t-100) cc_final: 0.6461 (t-100) REVERT: A 654 MET cc_start: 0.0858 (mmp) cc_final: 0.0536 (mmm) REVERT: A 751 LEU cc_start: 0.8364 (pp) cc_final: 0.7978 (tp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1589 time to fit residues: 23.6272 Evaluate side-chains 100 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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: 0.4762 moved from start: 0.7171 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= 0.219 Angle : 0.732 7.123 7672 Z= 0.379 Chirality : 0.044 0.197 917 Planarity : 0.006 0.069 969 Dihedral : 4.966 25.905 770 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: 0.38 (0.32), residues: 721 helix: 1.08 (0.24), residues: 483 sheet: -1.11 (0.69), residues: 31 loop : -1.44 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 737 HIS 0.009 0.002 HIS A 132 PHE 0.048 0.002 PHE A 649 TYR 0.017 0.002 TYR A 10 ARG 0.010 0.001 ARG A 463 *********************** 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 107 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.599 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS A 748 " (corrupted residue). Skipping it. REVERT: A 2 PHE cc_start: 0.6279 (m-80) cc_final: 0.4613 (m-80) REVERT: A 20 MET cc_start: 0.6689 (tmm) cc_final: 0.6187 (tpt) REVERT: A 130 LEU cc_start: 0.8094 (mp) cc_final: 0.7223 (tp) REVERT: A 146 GLU cc_start: 0.8874 (mp0) cc_final: 0.8670 (mp0) REVERT: A 463 ARG cc_start: 0.7395 (ptp-110) cc_final: 0.7154 (ptp-110) REVERT: A 563 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8628 (mmmt) REVERT: A 566 LEU cc_start: 0.8327 (mt) cc_final: 0.7953 (mp) REVERT: A 640 TRP cc_start: 0.7065 (t-100) cc_final: 0.6536 (t-100) REVERT: A 649 PHE cc_start: 0.7559 (m-80) cc_final: 0.7010 (m-80) REVERT: A 654 MET cc_start: 0.0781 (mmp) cc_final: 0.0456 (mmm) REVERT: A 728 MET cc_start: 0.6845 (ttt) cc_final: 0.6609 (tmm) REVERT: A 751 LEU cc_start: 0.8343 (pp) cc_final: 0.7822 (tp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1503 time to fit residues: 21.6377 Evaluate side-chains 104 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 30.0000 chunk 47 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.4818 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5639 Z= 0.265 Angle : 0.786 7.819 7672 Z= 0.409 Chirality : 0.045 0.199 917 Planarity : 0.007 0.081 969 Dihedral : 5.253 34.139 770 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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 : 0.15 % 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: 0.21 (0.31), residues: 721 helix: 0.99 (0.24), residues: 475 sheet: -1.43 (0.69), residues: 31 loop : -1.49 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 737 HIS 0.008 0.002 HIS A 132 PHE 0.033 0.002 PHE A 649 TYR 0.021 0.003 TYR A 30 ARG 0.009 0.001 ARG A 463 ********************** 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 107 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.627 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. REVERT: A 2 PHE cc_start: 0.6388 (m-80) cc_final: 0.3729 (m-80) REVERT: A 20 MET cc_start: 0.6737 (tmm) cc_final: 0.6303 (tpt) REVERT: A 130 LEU cc_start: 0.8281 (mp) cc_final: 0.7298 (tp) REVERT: A 146 GLU cc_start: 0.8855 (mp0) cc_final: 0.8630 (mp0) REVERT: A 398 MET cc_start: 0.0621 (tpp) cc_final: 0.0321 (tpp) REVERT: A 563 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8626 (mmmt) REVERT: A 566 LEU cc_start: 0.8330 (mt) cc_final: 0.8021 (mt) REVERT: A 579 MET cc_start: 0.8052 (mmt) cc_final: 0.7818 (mmm) REVERT: A 640 TRP cc_start: 0.7115 (t-100) cc_final: 0.6580 (t-100) REVERT: A 649 PHE cc_start: 0.7762 (m-80) cc_final: 0.7229 (m-80) REVERT: A 654 MET cc_start: 0.0665 (mmp) cc_final: 0.0288 (mmm) REVERT: A 704 LEU cc_start: 0.7485 (mm) cc_final: 0.7049 (mm) REVERT: A 728 MET cc_start: 0.6765 (ttt) cc_final: 0.6547 (ttp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1535 time to fit residues: 22.2067 Evaluate side-chains 100 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.5020 r_free = 0.5020 target = 0.297303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.273986 restraints weight = 9406.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.277767 restraints weight = 9799.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.279122 restraints weight = 6195.269| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5055 moved from start: 0.7758 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= 0.227 Angle : 0.764 9.278 7672 Z= 0.392 Chirality : 0.044 0.197 917 Planarity : 0.006 0.069 969 Dihedral : 5.112 29.760 770 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: 0.20 (0.31), residues: 721 helix: 1.00 (0.24), residues: 475 sheet: -1.24 (0.97), residues: 21 loop : -1.56 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 737 HIS 0.008 0.002 HIS A 132 PHE 0.030 0.002 PHE A 649 TYR 0.017 0.002 TYR A 10 ARG 0.009 0.001 ARG A 463 =============================================================================== Job complete usr+sys time: 1180.76 seconds wall clock time: 21 minutes 58.51 seconds (1318.51 seconds total)