Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:47:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bzy_16345/04_2023/8bzy_16345_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 2817 2.51 5 N 702 2.21 5 O 759 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4311 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'PLC': 1, 'SZU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 2.97, per 1000 atoms: 0.69 Number of scatterers: 4311 At special positions: 0 Unit cell: (89.838, 87.885, 69.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 1 15.00 F 1 9.00 O 759 8.00 N 702 7.00 C 2817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 637.2 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 3 sheets defined 68.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 19 through 22 Processing helix chain 'A' and resid 24 through 53 Processing helix chain 'A' and resid 58 through 85 removed outlier: 5.331A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 126 through 163 removed outlier: 4.025A pdb=" N THR A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 198 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 removed outlier: 3.730A pdb=" N VAL A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.647A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.855A pdb=" N TYR A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.958A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'A' and resid 452 through 483 removed outlier: 4.232A pdb=" N SER A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 513 removed outlier: 3.739A pdb=" N ARG A 489 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 545 removed outlier: 6.332A pdb=" N GLY A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.187A pdb=" N GLU B 33 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA B 40 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG B 45 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 97 through 103 removed outlier: 5.791A pdb=" N TYR B 108 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 102 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 816 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: 1.34 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 654 1.31 - 1.43: 1236 1.43 - 1.56: 2462 1.56 - 1.68: 2 1.68 - 1.81: 52 Bond restraints: 4406 Sorted by residual: bond pdb=" C21 SZU A 602 " pdb=" N5 SZU A 602 " ideal model delta sigma weight residual 1.282 1.361 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C5 SZU A 602 " pdb=" C6 SZU A 602 " ideal model delta sigma weight residual 1.309 1.386 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C1 SZU A 602 " pdb=" O1 SZU A 602 " ideal model delta sigma weight residual 1.256 1.184 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C4 SZU A 602 " pdb=" C5 SZU A 602 " ideal model delta sigma weight residual 1.441 1.384 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " ideal model delta sigma weight residual 1.579 1.524 0.055 2.00e-02 2.50e+03 7.67e+00 ... (remaining 4401 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 102 107.09 - 113.81: 2551 113.81 - 120.54: 1725 120.54 - 127.27: 1559 127.27 - 133.99: 51 Bond angle restraints: 5988 Sorted by residual: angle pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N4 SZU A 602 " ideal model delta sigma weight residual 145.49 125.39 20.10 3.00e+00 1.11e-01 4.49e+01 angle pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N5 SZU A 602 " ideal model delta sigma weight residual 105.25 124.73 -19.48 3.00e+00 1.11e-01 4.22e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 103.55 -9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C6 SZU A 602 " pdb=" C7 SZU A 602 " pdb=" F1 SZU A 602 " ideal model delta sigma weight residual 110.47 120.40 -9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C3 SZU A 602 " pdb=" C7 SZU A 602 " pdb=" F1 SZU A 602 " ideal model delta sigma weight residual 129.72 121.01 8.71 3.00e+00 1.11e-01 8.44e+00 ... (remaining 5983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.62: 2466 25.62 - 51.24: 62 51.24 - 76.86: 4 76.86 - 102.48: 0 102.48 - 128.10: 1 Dihedral angle restraints: 2533 sinusoidal: 959 harmonic: 1574 Sorted by residual: dihedral pdb=" C13 SZU A 602 " pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N5 SZU A 602 " ideal model delta sinusoidal sigma weight residual -163.43 -35.33 -128.10 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" N LEU A 129 " pdb=" CA LEU A 129 " pdb=" CB LEU A 129 " pdb=" CG LEU A 129 " ideal model delta sinusoidal sigma weight residual -60.00 -114.93 54.93 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sinusoidal sigma weight residual -60.00 -111.55 51.55 3 1.50e+01 4.44e-03 9.02e+00 ... (remaining 2530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 387 0.025 - 0.050: 193 0.050 - 0.075: 79 0.075 - 0.100: 29 0.100 - 0.125: 9 Chirality restraints: 697 Sorted by residual: chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" C2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C3 PLC A 601 " pdb=" O2 PLC A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.44 0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL B 79 " pdb=" N VAL B 79 " pdb=" C VAL B 79 " pdb=" CB VAL B 79 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.92e-01 ... (remaining 694 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C GLN A 155 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN A 155 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 156 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 525 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C LEU A 525 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 525 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 526 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 527 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C SER A 527 " 0.028 2.00e-02 2.50e+03 pdb=" O SER A 527 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 528 " -0.009 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1238 2.82 - 3.34: 4411 3.34 - 3.86: 7367 3.86 - 4.38: 8166 4.38 - 4.90: 14663 Nonbonded interactions: 35845 Sorted by model distance: nonbonded pdb=" O ALA B 52 " pdb=" NH1 ARG B 72 " model vdw 2.297 2.520 nonbonded pdb=" OG SER A 390 " pdb=" O SER A 454 " model vdw 2.339 2.440 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.361 2.520 nonbonded pdb=" O VAL B 29 " pdb=" NH2 ARG B 72 " model vdw 2.398 2.520 nonbonded pdb=" O LEU A 60 " pdb=" OH TYR A 133 " model vdw 2.407 2.440 ... (remaining 35840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.590 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.005 0.079 4406 Z= 0.305 Angle : 0.659 20.104 5988 Z= 0.299 Chirality : 0.037 0.125 697 Planarity : 0.004 0.026 725 Dihedral : 11.454 128.102 1526 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.42 % 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: 2.10 (0.37), residues: 541 helix: 2.49 (0.27), residues: 366 sheet: 0.15 (0.76), residues: 40 loop : -1.43 (0.54), residues: 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.482 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.1925 time to fit residues: 11.6712 Evaluate side-chains 45 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0498 time to fit residues: 1.3757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 228 GLN B 13 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4406 Z= 0.252 Angle : 0.494 8.681 5988 Z= 0.266 Chirality : 0.037 0.118 697 Planarity : 0.005 0.027 725 Dihedral : 7.539 84.572 619 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.54 % 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: 1.65 (0.36), residues: 541 helix: 2.08 (0.26), residues: 367 sheet: -0.11 (0.73), residues: 40 loop : -1.34 (0.53), residues: 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.493 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.1795 time to fit residues: 10.7085 Evaluate side-chains 42 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0455 time to fit residues: 0.8928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 4406 Z= 0.225 Angle : 0.472 8.133 5988 Z= 0.254 Chirality : 0.036 0.126 697 Planarity : 0.004 0.026 725 Dihedral : 7.252 76.122 619 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.54 % 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: 1.62 (0.36), residues: 541 helix: 2.07 (0.26), residues: 366 sheet: -0.08 (0.72), residues: 40 loop : -1.39 (0.52), residues: 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.427 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.1870 time to fit residues: 10.6098 Evaluate side-chains 43 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0530 time to fit residues: 1.0397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4406 Z= 0.168 Angle : 0.437 7.305 5988 Z= 0.237 Chirality : 0.035 0.123 697 Planarity : 0.004 0.026 725 Dihedral : 6.727 65.031 619 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.32 % 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: 1.81 (0.36), residues: 541 helix: 2.24 (0.26), residues: 366 sheet: -0.03 (0.71), residues: 40 loop : -1.40 (0.52), residues: 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.470 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.1841 time to fit residues: 10.9117 Evaluate side-chains 41 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0474 time to fit residues: 0.8160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4406 Z= 0.220 Angle : 0.464 7.801 5988 Z= 0.250 Chirality : 0.036 0.121 697 Planarity : 0.004 0.026 725 Dihedral : 6.661 57.135 619 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.35), residues: 541 helix: 2.13 (0.26), residues: 367 sheet: 0.38 (0.71), residues: 46 loop : -1.57 (0.52), residues: 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.466 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 48 average time/residue: 0.2016 time to fit residues: 12.2430 Evaluate side-chains 46 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0519 time to fit residues: 1.3947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4406 Z= 0.227 Angle : 0.479 9.199 5988 Z= 0.256 Chirality : 0.036 0.122 697 Planarity : 0.004 0.026 725 Dihedral : 6.588 52.678 619 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.32 % 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: 1.68 (0.35), residues: 541 helix: 2.13 (0.26), residues: 366 sheet: 0.21 (0.71), residues: 46 loop : -1.61 (0.52), residues: 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.486 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.2076 time to fit residues: 11.3277 Evaluate side-chains 40 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0477 time to fit residues: 0.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 43 optimal weight: 0.0020 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4406 Z= 0.176 Angle : 0.458 8.355 5988 Z= 0.246 Chirality : 0.035 0.121 697 Planarity : 0.004 0.026 725 Dihedral : 6.216 47.785 619 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.10 % 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: 1.88 (0.36), residues: 541 helix: 2.28 (0.26), residues: 366 sheet: 0.26 (0.70), residues: 46 loop : -1.52 (0.53), residues: 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.470 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.1954 time to fit residues: 10.1110 Evaluate side-chains 41 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0445 time to fit residues: 0.8886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4406 Z= 0.196 Angle : 0.467 8.548 5988 Z= 0.251 Chirality : 0.036 0.121 697 Planarity : 0.004 0.027 725 Dihedral : 6.187 46.433 619 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.88 % 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: 1.91 (0.36), residues: 541 helix: 2.29 (0.26), residues: 366 sheet: 0.31 (0.71), residues: 46 loop : -1.49 (0.53), residues: 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.351 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 43 average time/residue: 0.2081 time to fit residues: 11.3082 Evaluate side-chains 39 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.0970 chunk 43 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4406 Z= 0.168 Angle : 0.453 7.899 5988 Z= 0.244 Chirality : 0.035 0.121 697 Planarity : 0.004 0.026 725 Dihedral : 5.976 46.173 619 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.22 % 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: 2.02 (0.36), residues: 541 helix: 2.38 (0.26), residues: 366 sheet: 0.34 (0.71), residues: 46 loop : -1.45 (0.53), residues: 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.461 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2142 time to fit residues: 11.4206 Evaluate side-chains 40 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4406 Z= 0.249 Angle : 0.512 9.228 5988 Z= 0.271 Chirality : 0.037 0.122 697 Planarity : 0.004 0.026 725 Dihedral : 6.355 46.990 619 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.66 % 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: 1.80 (0.36), residues: 541 helix: 2.15 (0.26), residues: 367 sheet: 0.34 (0.71), residues: 46 loop : -1.38 (0.53), residues: 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.400 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.1920 time to fit residues: 9.9624 Evaluate side-chains 41 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0481 time to fit residues: 0.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 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 = 0.3419 r_free = 0.3419 target = 0.132834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.101796 restraints weight = 4546.665| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.82 r_work: 0.2927 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4406 Z= 0.233 Angle : 0.513 8.860 5988 Z= 0.271 Chirality : 0.036 0.123 697 Planarity : 0.004 0.026 725 Dihedral : 6.406 47.453 619 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.44 % 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: 1.79 (0.36), residues: 541 helix: 2.15 (0.26), residues: 367 sheet: 0.30 (0.71), residues: 46 loop : -1.38 (0.54), residues: 128 =============================================================================== Job complete usr+sys time: 1295.00 seconds wall clock time: 24 minutes 13.17 seconds (1453.17 seconds total)