Starting phenix.real_space_refine on Thu Dec 7 19:04:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2023/6zpg_11338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2023/6zpg_11338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2023/6zpg_11338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2023/6zpg_11338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2023/6zpg_11338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpg_11338/12_2023/6zpg_11338.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 2440 2.51 5 N 657 2.21 5 O 687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3808 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3808 Classifications: {'peptide': 463} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 449} Chain breaks: 8 Time building chain proxies: 2.44, per 1000 atoms: 0.64 Number of scatterers: 3808 At special positions: 0 Unit cell: (90.741, 124.117, 65.709, 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 24 16.00 O 687 8.00 N 657 7.00 C 2440 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: 1.42 Conformation dependent library (CDL) restraints added in 789.0 milliseconds 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.245A pdb=" N GLY A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 109 removed outlier: 3.739A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.723A pdb=" N GLU A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 175 Processing helix chain 'A' and resid 200 through 221 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 249 through 263 Processing helix chain 'A' and resid 266 through 282 Processing helix chain 'A' and resid 305 through 330 Processing helix chain 'A' and resid 393 through 413 Processing helix chain 'A' and resid 416 through 433 Processing helix chain 'A' and resid 437 through 455 removed outlier: 4.011A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 463 through 495 Processing helix chain 'A' and resid 499 through 523 Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.561A pdb=" N MET A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 584 Processing helix chain 'A' and resid 589 through 607 309 hydrogen bonds defined for protein. 927 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: 0.97 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1229 1.34 - 1.46: 771 1.46 - 1.58: 1844 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 3881 Sorted by residual: bond pdb=" C ARG A 541 " pdb=" N PRO A 542 " ideal model delta sigma weight residual 1.336 1.395 -0.059 1.23e-02 6.61e+03 2.34e+01 bond pdb=" N GLU A 175 " pdb=" CA GLU A 175 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.50e+00 bond pdb=" C ASP A 497 " pdb=" N PRO A 498 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C ASP A 526 " pdb=" N PRO A 527 " ideal model delta sigma weight residual 1.341 1.361 -0.020 1.60e-02 3.91e+03 1.61e+00 bond pdb=" CB GLN A 282 " pdb=" CG GLN A 282 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 ... (remaining 3876 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.51: 53 105.51 - 113.17: 2081 113.17 - 120.83: 2038 120.83 - 128.49: 1016 128.49 - 136.15: 34 Bond angle restraints: 5222 Sorted by residual: angle pdb=" C GLU A 222 " pdb=" N MET A 223 " pdb=" CA MET A 223 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C GLY A 414 " pdb=" N TYR A 415 " pdb=" CA TYR A 415 " ideal model delta sigma weight residual 121.70 128.25 -6.55 1.80e+00 3.09e-01 1.32e+01 angle pdb=" C GLU A 175 " pdb=" N VAL A 176 " pdb=" CA VAL A 176 " ideal model delta sigma weight residual 121.70 127.98 -6.28 1.80e+00 3.09e-01 1.22e+01 angle pdb=" C HIS A 304 " pdb=" N GLN A 305 " pdb=" CA GLN A 305 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.05e+01 angle pdb=" N LEU A 607 " pdb=" CA LEU A 607 " pdb=" C LEU A 607 " ideal model delta sigma weight residual 109.81 116.98 -7.17 2.21e+00 2.05e-01 1.05e+01 ... (remaining 5217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 2027 15.79 - 31.58: 248 31.58 - 47.37: 69 47.37 - 63.15: 13 63.15 - 78.94: 8 Dihedral angle restraints: 2365 sinusoidal: 982 harmonic: 1383 Sorted by residual: dihedral pdb=" CA MET A 223 " pdb=" C MET A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY A 555 " pdb=" C GLY A 555 " pdb=" N LYS A 556 " pdb=" CA LYS A 556 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP A 561 " pdb=" C ASP A 561 " pdb=" N PRO A 562 " pdb=" CA PRO A 562 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 2362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 444 0.056 - 0.111: 103 0.111 - 0.167: 23 0.167 - 0.222: 4 0.222 - 0.278: 1 Chirality restraints: 575 Sorted by residual: chirality pdb=" CB ILE A 139 " pdb=" CA ILE A 139 " pdb=" CG1 ILE A 139 " pdb=" CG2 ILE A 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA GLU A 455 " pdb=" N GLU A 455 " pdb=" C GLU A 455 " pdb=" CB GLU A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 572 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 607 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO A 608 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 608 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 608 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 593 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE A 593 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 593 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 594 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 9 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C VAL A 9 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL A 9 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 10 " 0.009 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1111 2.83 - 3.35: 3743 3.35 - 3.86: 6350 3.86 - 4.38: 6773 4.38 - 4.90: 11211 Nonbonded interactions: 29188 Sorted by model distance: nonbonded pdb=" OH TYR A 481 " pdb=" OD1 ASN A 510 " model vdw 2.313 2.440 nonbonded pdb=" O GLN A 197 " pdb=" OG SER A 200 " model vdw 2.341 2.440 nonbonded pdb=" O LEU A 606 " pdb=" OG1 THR A 609 " model vdw 2.359 2.440 nonbonded pdb=" O SER A 35 " pdb=" OG SER A 38 " model vdw 2.360 2.440 nonbonded pdb=" O TYR A 317 " pdb=" OG1 THR A 320 " model vdw 2.409 2.440 ... (remaining 29183 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.470 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.540 Find NCS groups from input model: 0.100 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 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 0.059 3881 Z= 0.248 Angle : 0.987 11.151 5222 Z= 0.494 Chirality : 0.052 0.278 575 Planarity : 0.006 0.049 660 Dihedral : 15.638 78.940 1461 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.25 % Allowed : 6.88 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -3.85 (0.31), residues: 445 helix: -1.84 (0.20), residues: 379 sheet: None (None), residues: 0 loop : -5.66 (0.50), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 314 HIS 0.013 0.001 HIS A 447 PHE 0.011 0.001 PHE A 409 TYR 0.015 0.001 TYR A 576 ARG 0.001 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2410 time to fit residues: 41.3888 Evaluate side-chains 90 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0350 time to fit residues: 0.6691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 HIS A 324 ASN A 330 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3881 Z= 0.192 Angle : 0.722 7.333 5222 Z= 0.370 Chirality : 0.040 0.143 575 Planarity : 0.005 0.042 660 Dihedral : 5.223 22.365 505 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.25 % Allowed : 4.18 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.97 (0.38), residues: 445 helix: 0.14 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -5.25 (0.55), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 314 HIS 0.011 0.001 HIS A 447 PHE 0.008 0.001 PHE A 409 TYR 0.022 0.002 TYR A 576 ARG 0.007 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2095 time to fit residues: 27.2555 Evaluate side-chains 78 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 232 HIS A 252 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3881 Z= 0.158 Angle : 0.724 10.646 5222 Z= 0.357 Chirality : 0.040 0.133 575 Planarity : 0.004 0.044 660 Dihedral : 4.994 20.772 505 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.09 (0.39), residues: 445 helix: 0.77 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -5.29 (0.53), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.011 0.001 HIS A 447 PHE 0.022 0.001 PHE A 475 TYR 0.022 0.002 TYR A 576 ARG 0.004 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2039 time to fit residues: 25.2550 Evaluate side-chains 80 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 324 ASN A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3881 Z= 0.196 Angle : 0.723 9.271 5222 Z= 0.369 Chirality : 0.041 0.133 575 Planarity : 0.005 0.051 660 Dihedral : 5.049 21.787 505 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.40), residues: 445 helix: 0.99 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -5.34 (0.51), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 149 HIS 0.010 0.001 HIS A 447 PHE 0.020 0.002 PHE A 409 TYR 0.030 0.002 TYR A 516 ARG 0.004 0.001 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1868 time to fit residues: 22.3840 Evaluate side-chains 73 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.0270 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3881 Z= 0.214 Angle : 0.766 7.651 5222 Z= 0.389 Chirality : 0.043 0.137 575 Planarity : 0.005 0.042 660 Dihedral : 5.197 21.492 505 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.24 (0.39), residues: 445 helix: 1.03 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -4.96 (0.53), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 149 HIS 0.010 0.002 HIS A 447 PHE 0.019 0.002 PHE A 409 TYR 0.028 0.002 TYR A 576 ARG 0.004 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2107 time to fit residues: 27.1640 Evaluate side-chains 88 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.7516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3881 Z= 0.166 Angle : 0.744 8.651 5222 Z= 0.370 Chirality : 0.042 0.131 575 Planarity : 0.004 0.047 660 Dihedral : 5.084 19.864 505 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.40), residues: 445 helix: 1.15 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -5.12 (0.52), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 149 HIS 0.012 0.001 HIS A 447 PHE 0.015 0.001 PHE A 475 TYR 0.027 0.002 TYR A 576 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2027 time to fit residues: 24.4205 Evaluate side-chains 82 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.0980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 252 ASN A 324 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3881 Z= 0.175 Angle : 0.759 7.806 5222 Z= 0.382 Chirality : 0.043 0.205 575 Planarity : 0.004 0.048 660 Dihedral : 5.047 19.458 505 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.40), residues: 445 helix: 1.10 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -5.02 (0.54), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 149 HIS 0.015 0.002 HIS A 209 PHE 0.020 0.002 PHE A 203 TYR 0.025 0.002 TYR A 576 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1972 time to fit residues: 22.9616 Evaluate side-chains 82 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 470 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.8061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3881 Z= 0.183 Angle : 0.766 7.658 5222 Z= 0.386 Chirality : 0.044 0.177 575 Planarity : 0.004 0.047 660 Dihedral : 5.015 19.077 505 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.45 (0.40), residues: 445 helix: 1.15 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -4.89 (0.55), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 149 HIS 0.013 0.002 HIS A 447 PHE 0.016 0.002 PHE A 203 TYR 0.025 0.002 TYR A 576 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2102 time to fit residues: 24.0469 Evaluate side-chains 77 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.8291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3881 Z= 0.199 Angle : 0.800 7.663 5222 Z= 0.407 Chirality : 0.045 0.186 575 Planarity : 0.004 0.047 660 Dihedral : 5.026 19.056 505 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.37 (0.40), residues: 445 helix: 1.06 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -4.83 (0.58), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 149 HIS 0.014 0.001 HIS A 447 PHE 0.027 0.002 PHE A 13 TYR 0.024 0.002 TYR A 576 ARG 0.004 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1853 time to fit residues: 20.8096 Evaluate side-chains 75 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.8464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3881 Z= 0.196 Angle : 0.801 7.594 5222 Z= 0.408 Chirality : 0.045 0.196 575 Planarity : 0.004 0.047 660 Dihedral : 4.990 19.129 505 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.50 (0.40), residues: 445 helix: 1.15 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -4.63 (0.58), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 149 HIS 0.015 0.002 HIS A 209 PHE 0.054 0.002 PHE A 13 TYR 0.026 0.002 TYR A 207 ARG 0.004 0.000 ARG A 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1933 time to fit residues: 20.8708 Evaluate side-chains 80 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.144881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.120414 restraints weight = 15370.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.122885 restraints weight = 12597.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124656 restraints weight = 10643.448| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.8812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3881 Z= 0.200 Angle : 0.791 7.884 5222 Z= 0.404 Chirality : 0.044 0.173 575 Planarity : 0.004 0.047 660 Dihedral : 4.981 19.258 505 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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 (0.40), residues: 445 helix: 1.06 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -4.70 (0.58), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 149 HIS 0.015 0.001 HIS A 447 PHE 0.041 0.002 PHE A 13 TYR 0.021 0.002 TYR A 402 ARG 0.004 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1174.01 seconds wall clock time: 21 minutes 58.65 seconds (1318.65 seconds total)