Starting phenix.real_space_refine on Fri Aug 2 20:04:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b56_44201/08_2024/9b56_44201.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b56_44201/08_2024/9b56_44201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b56_44201/08_2024/9b56_44201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b56_44201/08_2024/9b56_44201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b56_44201/08_2024/9b56_44201.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b56_44201/08_2024/9b56_44201.cif" } resolution = 3.35 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= 0.041 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 14 5.16 5 C 3110 2.51 5 N 824 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 3107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} Conformer: "B" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} bond proxies already assigned to first conformer: 3161 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.38, per 1000 atoms: 0.90 Number of scatterers: 4871 At special positions: 0 Unit cell: (62.776, 84.056, 104.272, 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 14 16.00 O 923 8.00 N 824 7.00 C 3110 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 48.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.736A pdb=" N VAL A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 307 through 311 removed outlier: 4.057A pdb=" N ALA C 311 " --> pdb=" O PRO C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 357 through 374 Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.517A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.313A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.651A pdb=" N TYR C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.896A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.725A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 533 removed outlier: 4.236A pdb=" N LEU C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.680A pdb=" N LEU C 538 " --> pdb=" O PRO C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 558 through 564 Processing helix chain 'C' and resid 574 through 586 removed outlier: 3.573A pdb=" N PHE C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 650 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 removed outlier: 9.105A pdb=" N LEU B 67 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE B 4 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 69 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 6 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 3.654A pdb=" N VAL C 321 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 479 removed outlier: 3.703A pdb=" N GLU C 482 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568 216 hydrogen bonds defined for protein. 605 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: 1.26 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: 1.13 - 1.27: 820 1.27 - 1.41: 1238 1.41 - 1.54: 2895 1.54 - 1.68: 6 1.68 - 1.82: 24 Bond restraints: 4983 Sorted by residual: bond pdb=" C04 A1AIV B 101 " pdb=" C05 A1AIV B 101 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.132 0.019 2.00e-02 2.50e+03 9.43e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.45e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 100.48 - 116.30: 3300 116.30 - 132.13: 3438 132.13 - 147.95: 8 147.95 - 163.77: 0 163.77 - 179.60: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" N LEU C 424 " pdb=" CA LEU C 424 " pdb=" C LEU C 424 " ideal model delta sigma weight residual 109.79 107.20 2.59 1.56e+00 4.11e-01 2.75e+00 angle pdb=" N ARG A 90 " pdb=" CA ARG A 90 " pdb=" C ARG A 90 " ideal model delta sigma weight residual 110.80 114.14 -3.34 2.13e+00 2.20e-01 2.46e+00 angle pdb=" C PRO A 18 " pdb=" N SER A 19 " pdb=" CA SER A 19 " ideal model delta sigma weight residual 121.54 124.08 -2.54 1.91e+00 2.74e-01 1.77e+00 angle pdb=" C03 A1AIV B 101 " pdb=" C02 A1AIV B 101 " pdb=" N01 A1AIV B 101 " ideal model delta sigma weight residual 111.06 107.08 3.98 3.00e+00 1.11e-01 1.76e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 112.10 -2.76 2.08e+00 2.31e-01 1.76e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.09: 2684 12.09 - 24.17: 261 24.17 - 36.26: 55 36.26 - 48.35: 15 48.35 - 60.43: 3 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA LEU A 86 " pdb=" C LEU A 86 " pdb=" N ASP A 87 " pdb=" CA ASP A 87 " ideal model delta harmonic sigma weight residual 180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL C 515 " pdb=" C VAL C 515 " pdb=" N THR C 516 " pdb=" CA THR C 516 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR C 423 " pdb=" C TYR C 423 " pdb=" N LEU C 424 " pdb=" CA LEU C 424 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.08e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 450 0.028 - 0.055: 187 0.055 - 0.083: 57 0.083 - 0.110: 27 0.110 - 0.138: 16 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE C 533 " pdb=" N ILE C 533 " pdb=" C ILE C 533 " pdb=" CB ILE C 533 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 431 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 431 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 431 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 646 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO C 647 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 647 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 647 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 94 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 95 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.016 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 12 2.42 - 3.04: 3040 3.04 - 3.66: 6690 3.66 - 4.28: 10393 4.28 - 4.90: 17838 Nonbonded interactions: 37973 Sorted by model distance: nonbonded pdb=" SG CYS C 639 " pdb=" C03 A1AIV B 101 " model vdw 1.794 3.800 nonbonded pdb=" OE2 GLU A 9 " pdb=" OH TYR A 60 " model vdw 2.285 3.040 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.317 3.040 nonbonded pdb=" N CYS A 85 " pdb=" O GLY B 75 " model vdw 2.333 3.120 nonbonded pdb=" NH1 ARG C 323 " pdb=" OE2 GLU C 364 " model vdw 2.341 3.120 ... (remaining 37968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.48 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: 1.410 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.003 0.073 4983 Z= 0.190 Angle : 0.463 3.985 6747 Z= 0.232 Chirality : 0.039 0.138 737 Planarity : 0.003 0.033 873 Dihedral : 10.297 60.433 1878 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.29 % Allowed : 6.63 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.28 (0.36), residues: 594 helix: 1.52 (0.34), residues: 247 sheet: 1.38 (0.62), residues: 83 loop : 0.12 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.001 0.000 HIS C 420 PHE 0.009 0.001 PHE C 407 TYR 0.010 0.001 TYR C 419 ARG 0.002 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8069 (mttp) REVERT: C 613 MET cc_start: 0.8855 (ttt) cc_final: 0.8532 (ttt) REVERT: C 632 GLN cc_start: 0.8251 (mt0) cc_final: 0.8015 (mt0) outliers start: 7 outliers final: 5 residues processed: 89 average time/residue: 0.2108 time to fit residues: 23.1757 Evaluate side-chains 59 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 466 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.0010 chunk 17 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4983 Z= 0.180 Angle : 0.515 6.087 6747 Z= 0.266 Chirality : 0.041 0.129 737 Planarity : 0.004 0.036 873 Dihedral : 5.702 49.181 670 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.29 % Allowed : 11.97 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.32 (0.36), residues: 594 helix: 1.63 (0.34), residues: 255 sheet: 1.39 (0.61), residues: 83 loop : 0.00 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.001 0.000 HIS C 420 PHE 0.021 0.002 PHE B 45 TYR 0.009 0.001 TYR C 419 ARG 0.007 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8338 (mtpp) cc_final: 0.8071 (mttp) REVERT: C 329 ASP cc_start: 0.7477 (m-30) cc_final: 0.7240 (m-30) REVERT: C 613 MET cc_start: 0.8960 (ttt) cc_final: 0.8660 (ttt) REVERT: C 632 GLN cc_start: 0.8245 (mt0) cc_final: 0.7999 (mt0) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1906 time to fit residues: 15.1167 Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 52 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4983 Z= 0.239 Angle : 0.519 5.451 6747 Z= 0.269 Chirality : 0.042 0.189 737 Planarity : 0.004 0.035 873 Dihedral : 5.357 46.285 668 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.47 % Allowed : 12.15 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.36), residues: 594 helix: 1.53 (0.34), residues: 257 sheet: 1.22 (0.60), residues: 85 loop : -0.03 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.001 0.000 HIS C 420 PHE 0.021 0.002 PHE B 45 TYR 0.012 0.001 TYR C 419 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8052 (mttp) REVERT: A 90 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7587 (ttp-110) REVERT: A 114 ASN cc_start: 0.7234 (t0) cc_final: 0.6869 (t0) REVERT: A 140 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7755 (mm-30) REVERT: C 329 ASP cc_start: 0.7564 (m-30) cc_final: 0.7290 (m-30) REVERT: C 613 MET cc_start: 0.9001 (ttt) cc_final: 0.8735 (ttt) REVERT: C 632 GLN cc_start: 0.8237 (mt0) cc_final: 0.7982 (mt0) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.2035 time to fit residues: 14.7725 Evaluate side-chains 53 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 466 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4983 Z= 0.296 Angle : 0.551 8.103 6747 Z= 0.281 Chirality : 0.043 0.160 737 Planarity : 0.004 0.035 873 Dihedral : 5.187 47.049 666 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.76 % Allowed : 11.79 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.03 (0.36), residues: 594 helix: 1.45 (0.34), residues: 256 sheet: 1.07 (0.59), residues: 85 loop : -0.18 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS A 75 PHE 0.022 0.002 PHE B 45 TYR 0.013 0.001 TYR C 419 ARG 0.009 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8063 (mttp) REVERT: A 99 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7189 (tp) REVERT: B 73 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5972 (pt) REVERT: C 329 ASP cc_start: 0.7675 (m-30) cc_final: 0.7392 (m-30) REVERT: C 613 MET cc_start: 0.8992 (ttt) cc_final: 0.8726 (ttt) REVERT: C 632 GLN cc_start: 0.8251 (mt0) cc_final: 0.8004 (mt0) outliers start: 15 outliers final: 9 residues processed: 62 average time/residue: 0.1854 time to fit residues: 14.7734 Evaluate side-chains 59 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 466 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.0050 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 overall best weight: 0.3852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4983 Z= 0.180 Angle : 0.517 7.993 6747 Z= 0.262 Chirality : 0.041 0.153 737 Planarity : 0.004 0.035 873 Dihedral : 5.076 46.611 666 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.58 % Allowed : 12.34 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.36), residues: 594 helix: 1.57 (0.34), residues: 255 sheet: 1.41 (0.61), residues: 81 loop : -0.13 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.000 HIS C 420 PHE 0.012 0.001 PHE B 45 TYR 0.016 0.001 TYR A 74 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8054 (mttp) REVERT: A 143 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7754 (ttp80) REVERT: C 329 ASP cc_start: 0.7555 (m-30) cc_final: 0.7319 (m-30) REVERT: C 632 GLN cc_start: 0.8233 (mt0) cc_final: 0.7983 (mt0) outliers start: 14 outliers final: 9 residues processed: 63 average time/residue: 0.1916 time to fit residues: 15.4946 Evaluate side-chains 60 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 466 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4983 Z= 0.282 Angle : 0.556 9.520 6747 Z= 0.282 Chirality : 0.043 0.158 737 Planarity : 0.004 0.035 873 Dihedral : 5.175 46.924 666 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.39 % Allowed : 13.44 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.06 (0.36), residues: 594 helix: 1.54 (0.34), residues: 254 sheet: 1.23 (0.60), residues: 83 loop : -0.27 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS A 75 PHE 0.011 0.002 PHE C 365 TYR 0.012 0.001 TYR C 419 ARG 0.003 0.000 ARG C 568 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8064 (mttp) REVERT: A 90 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7101 (ttp-110) REVERT: A 99 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7190 (tp) REVERT: C 329 ASP cc_start: 0.7688 (m-30) cc_final: 0.7394 (m-30) REVERT: C 613 MET cc_start: 0.8981 (ttt) cc_final: 0.8718 (ttt) REVERT: C 632 GLN cc_start: 0.8254 (mt0) cc_final: 0.8007 (mt0) outliers start: 13 outliers final: 11 residues processed: 59 average time/residue: 0.1938 time to fit residues: 14.5646 Evaluate side-chains 60 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 516 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 33 optimal weight: 0.0980 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4983 Z= 0.173 Angle : 0.525 8.429 6747 Z= 0.267 Chirality : 0.041 0.150 737 Planarity : 0.004 0.036 873 Dihedral : 4.964 46.499 666 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.84 % Allowed : 13.44 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.36), residues: 594 helix: 1.62 (0.33), residues: 256 sheet: 1.34 (0.60), residues: 81 loop : -0.17 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.001 HIS B 68 PHE 0.021 0.001 PHE C 640 TYR 0.009 0.001 TYR C 419 ARG 0.006 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8081 (mttp) REVERT: A 99 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7137 (tp) REVERT: B 27 LYS cc_start: 0.4263 (pttp) cc_final: 0.3886 (pttm) REVERT: C 329 ASP cc_start: 0.7554 (m-30) cc_final: 0.7302 (m-30) REVERT: C 632 GLN cc_start: 0.8232 (mt0) cc_final: 0.7978 (mt0) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.2579 time to fit residues: 19.8815 Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 466 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.0030 chunk 31 optimal weight: 0.0770 chunk 22 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.1548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4983 Z= 0.125 Angle : 0.501 8.020 6747 Z= 0.255 Chirality : 0.040 0.168 737 Planarity : 0.004 0.036 873 Dihedral : 4.693 45.918 666 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 13.63 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.34 (0.36), residues: 594 helix: 1.79 (0.33), residues: 258 sheet: 1.42 (0.60), residues: 81 loop : -0.19 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 459 HIS 0.001 0.000 HIS C 512 PHE 0.012 0.001 PHE C 640 TYR 0.007 0.001 TYR C 419 ARG 0.007 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8092 (mttp) REVERT: C 329 ASP cc_start: 0.7402 (m-30) cc_final: 0.7133 (m-30) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.1826 time to fit residues: 14.1035 Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4983 Z= 0.234 Angle : 0.552 8.202 6747 Z= 0.285 Chirality : 0.042 0.192 737 Planarity : 0.004 0.035 873 Dihedral : 5.061 46.142 666 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.66 % Allowed : 14.18 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.24 (0.36), residues: 594 helix: 1.70 (0.34), residues: 256 sheet: 1.36 (0.59), residues: 81 loop : -0.21 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 PHE 0.012 0.001 PHE C 640 TYR 0.013 0.001 TYR A 145 ARG 0.005 0.000 ARG C 568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8119 (mttp) REVERT: C 329 ASP cc_start: 0.7538 (m-30) cc_final: 0.7279 (m-30) REVERT: C 613 MET cc_start: 0.8964 (ttm) cc_final: 0.8735 (ttt) outliers start: 9 outliers final: 9 residues processed: 53 average time/residue: 0.1787 time to fit residues: 12.5530 Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4983 Z= 0.224 Angle : 0.556 8.444 6747 Z= 0.285 Chirality : 0.042 0.241 737 Planarity : 0.004 0.038 873 Dihedral : 4.951 46.248 666 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.84 % Allowed : 14.18 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.19 (0.36), residues: 594 helix: 1.67 (0.33), residues: 256 sheet: 1.30 (0.59), residues: 81 loop : -0.23 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.002 0.001 HIS B 68 PHE 0.027 0.001 PHE B 45 TYR 0.013 0.001 TYR A 145 ARG 0.009 0.000 ARG A 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8116 (mttp) REVERT: A 99 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7142 (tp) REVERT: C 329 ASP cc_start: 0.7540 (m-30) cc_final: 0.7285 (m-30) REVERT: C 613 MET cc_start: 0.8967 (ttm) cc_final: 0.8739 (ttt) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1945 time to fit residues: 13.2810 Evaluate side-chains 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.0270 chunk 2 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 30 optimal weight: 0.0020 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 overall best weight: 0.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114597 restraints weight = 16112.480| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 4.90 r_work: 0.3284 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4983 Z= 0.135 Angle : 0.539 8.696 6747 Z= 0.276 Chirality : 0.041 0.184 737 Planarity : 0.004 0.036 873 Dihedral : 4.726 45.664 666 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.47 % Allowed : 14.73 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.37 (0.36), residues: 594 helix: 1.88 (0.33), residues: 258 sheet: 1.29 (0.58), residues: 81 loop : -0.18 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 459 HIS 0.002 0.001 HIS B 68 PHE 0.011 0.001 PHE B 45 TYR 0.016 0.001 TYR A 145 ARG 0.010 0.001 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1489.28 seconds wall clock time: 26 minutes 55.56 seconds (1615.56 seconds total)