Starting phenix.real_space_refine on Fri Aug 2 20:05:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b59_44204/08_2024/9b59_44204.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b59_44204/08_2024/9b59_44204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b59_44204/08_2024/9b59_44204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b59_44204/08_2024/9b59_44204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b59_44204/08_2024/9b59_44204.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b59_44204/08_2024/9b59_44204.cif" } resolution = 3.49 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= 0.040 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: 5.26, per 1000 atoms: 1.08 Number of scatterers: 4871 At special positions: 0 Unit cell: (70.224, 84.056, 97.888, 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: 1.97 Conformation dependent library (CDL) restraints added in 1.5 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: 29 helices and 6 sheets defined 48.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.687A 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 145 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'C' and resid 293 through 306 Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.848A 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: 3.520A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.520A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.612A 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: 3.920A 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: 3.628A pdb=" N ASN C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 495 " --> pdb=" O GLY C 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 491 through 495' Processing helix chain 'C' and resid 501 through 515 Processing helix chain 'C' and resid 518 through 531 Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.683A 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 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: 3.918A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 42 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 316 through 321 removed outlier: 5.769A pdb=" N LEU C 317 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ARG C 349 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU C 319 " --> pdb=" O ARG C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 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: 3.656A 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. 599 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: 2.05 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 - 1.40: 1233 1.40 - 1.54: 2867 1.54 - 1.68: 39 1.68 - 1.81: 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 1.32e+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 3.03e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.134 0.017 2.00e-02 2.50e+03 7.50e-01 bond pdb=" CG LEU C 595 " pdb=" CD2 LEU C 595 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.75e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 100.50 - 116.39: 3323 116.39 - 132.27: 3415 132.27 - 148.16: 8 148.16 - 164.04: 0 164.04 - 179.93: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" C PRO A 18 " pdb=" N SER A 19 " pdb=" CA SER A 19 " ideal model delta sigma weight residual 121.54 124.75 -3.21 1.91e+00 2.74e-01 2.83e+00 angle pdb=" N LEU C 424 " pdb=" CA LEU C 424 " pdb=" C LEU C 424 " ideal model delta sigma weight residual 109.79 107.23 2.56 1.56e+00 4.11e-01 2.69e+00 angle pdb=" N VAL C 515 " pdb=" CA VAL C 515 " pdb=" C VAL C 515 " ideal model delta sigma weight residual 109.34 112.35 -3.01 2.08e+00 2.31e-01 2.10e+00 angle pdb=" C TYR C 406 " pdb=" N PHE C 407 " pdb=" CA PHE C 407 " ideal model delta sigma weight residual 120.31 118.70 1.61 1.52e+00 4.33e-01 1.13e+00 angle pdb=" N SER C 569 " pdb=" CA SER C 569 " pdb=" CB SER C 569 " ideal model delta sigma weight residual 112.78 111.16 1.62 1.53e+00 4.27e-01 1.12e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.60: 2729 12.60 - 25.20: 235 25.20 - 37.79: 40 37.79 - 50.39: 12 50.39 - 62.99: 2 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: 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 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP C 357 " pdb=" CB ASP C 357 " pdb=" CG ASP C 357 " pdb=" OD1 ASP C 357 " ideal model delta sinusoidal sigma weight residual -30.00 -81.94 51.94 1 2.00e+01 2.50e-03 9.20e+00 dihedral pdb=" N LEU C 509 " pdb=" CA LEU C 509 " pdb=" CB LEU C 509 " pdb=" CG LEU C 509 " ideal model delta sinusoidal sigma weight residual -60.00 -105.55 45.55 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 471 0.029 - 0.058: 182 0.058 - 0.086: 45 0.086 - 0.115: 26 0.115 - 0.144: 13 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 2.58 -0.14 2.00e-01 2.50e+01 5.17e-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 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 84 " pdb=" N ILE A 84 " pdb=" C ILE A 84 " pdb=" CB ILE A 84 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 430 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+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 SER A 94 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.80e-01 pdb=" N PRO A 95 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 645 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.55e-01 pdb=" N PRO C 646 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 646 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 646 " -0.014 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 8 2.40 - 3.03: 2951 3.03 - 3.65: 6710 3.65 - 4.28: 10228 4.28 - 4.90: 17852 Nonbonded interactions: 37749 Sorted by model distance: nonbonded pdb=" SG CYS A 85 " pdb=" C03 A1AIV B 101 " model vdw 1.779 3.800 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 29 " model vdw 2.211 3.120 nonbonded pdb=" OG SER C 397 " pdb=" OE1 GLN C 521 " model vdw 2.240 3.040 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.314 3.040 nonbonded pdb=" O THR B 14 " pdb=" NZ LYS B 33 " model vdw 2.330 3.120 ... (remaining 37744 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=0.36 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: 2.600 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.340 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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= 0.174 Angle : 0.431 3.743 6747 Z= 0.217 Chirality : 0.038 0.144 737 Planarity : 0.003 0.032 873 Dihedral : 9.727 62.989 1878 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.74 % Allowed : 5.52 % Favored : 93.74 % 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: 1.74 (0.37), residues: 594 helix: 1.96 (0.34), residues: 247 sheet: 1.30 (0.62), residues: 86 loop : 0.42 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.001 0.000 HIS C 371 PHE 0.009 0.001 PHE C 407 TYR 0.008 0.001 TYR A 127 ARG 0.002 0.000 ARG C 642 *********************** 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 92 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7990 (t-90) cc_final: 0.7777 (t-90) REVERT: B 1 MET cc_start: 0.1243 (ptt) cc_final: 0.0701 (ptt) outliers start: 4 outliers final: 1 residues processed: 91 average time/residue: 0.2470 time to fit residues: 27.1554 Evaluate side-chains 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 29 optimal weight: 0.0270 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4983 Z= 0.179 Angle : 0.502 8.383 6747 Z= 0.264 Chirality : 0.041 0.161 737 Planarity : 0.004 0.036 873 Dihedral : 5.143 78.213 661 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.92 % Allowed : 9.02 % Favored : 90.06 % 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: 1.67 (0.37), residues: 594 helix: 1.81 (0.33), residues: 251 sheet: 1.39 (0.61), residues: 84 loop : 0.43 (0.43), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 141 HIS 0.003 0.001 HIS C 637 PHE 0.011 0.001 PHE C 365 TYR 0.009 0.001 TYR A 127 ARG 0.007 0.001 ARG C 568 *********************** 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 61 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7812 (mmm) cc_final: 0.7532 (mmm) REVERT: A 125 HIS cc_start: 0.8042 (t-90) cc_final: 0.7798 (t-90) REVERT: A 140 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 1 MET cc_start: 0.1106 (ptt) cc_final: 0.0254 (ptt) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.2148 time to fit residues: 16.3356 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 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: 0.7653 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4983 Z= 0.209 Angle : 0.513 9.321 6747 Z= 0.263 Chirality : 0.041 0.149 737 Planarity : 0.004 0.036 873 Dihedral : 4.996 73.379 661 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.66 % Allowed : 9.58 % Favored : 88.77 % 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: 1.63 (0.36), residues: 594 helix: 1.77 (0.33), residues: 251 sheet: 1.28 (0.61), residues: 84 loop : 0.43 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 141 HIS 0.003 0.000 HIS C 293 PHE 0.009 0.001 PHE C 522 TYR 0.012 0.001 TYR A 127 ARG 0.007 0.001 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 55 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7832 (mmm) cc_final: 0.7559 (mmm) REVERT: A 125 HIS cc_start: 0.7920 (t-90) cc_final: 0.7702 (t-90) REVERT: B 1 MET cc_start: 0.1410 (ptt) cc_final: 0.0470 (ptt) REVERT: B 74 ARG cc_start: 0.7938 (mmt180) cc_final: 0.7330 (ptt-90) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.2076 time to fit residues: 14.3263 Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.0060 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- 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: 0.7647 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4983 Z= 0.176 Angle : 0.489 9.933 6747 Z= 0.250 Chirality : 0.040 0.149 737 Planarity : 0.004 0.036 873 Dihedral : 4.964 73.042 661 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.66 % Allowed : 9.94 % Favored : 88.40 % 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: 1.56 (0.37), residues: 594 helix: 1.70 (0.33), residues: 258 sheet: 1.23 (0.60), residues: 84 loop : 0.38 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.001 0.000 HIS C 420 PHE 0.008 0.001 PHE C 522 TYR 0.012 0.001 TYR A 127 ARG 0.007 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 53 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7837 (mmm) cc_final: 0.7540 (mmm) REVERT: A 125 HIS cc_start: 0.7995 (t-90) cc_final: 0.7790 (t-90) REVERT: B 1 MET cc_start: 0.1198 (ptt) cc_final: 0.0310 (ptt) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.2094 time to fit residues: 13.9400 Evaluate side-chains 49 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 TRP 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: 0.9990 chunk 47 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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: 0.7678 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4983 Z= 0.263 Angle : 0.530 10.602 6747 Z= 0.268 Chirality : 0.041 0.144 737 Planarity : 0.004 0.035 873 Dihedral : 4.848 69.992 660 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.84 % Allowed : 10.13 % Favored : 88.03 % 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: 1.44 (0.36), residues: 594 helix: 1.57 (0.33), residues: 258 sheet: 1.16 (0.60), residues: 84 loop : 0.36 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS C 293 PHE 0.011 0.001 PHE C 522 TYR 0.013 0.001 TYR A 127 ARG 0.005 0.000 ARG A 143 *********************** 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 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7803 (mmm) cc_final: 0.7539 (mmm) REVERT: B 1 MET cc_start: 0.1251 (ptt) cc_final: 0.0518 (ptt) REVERT: B 74 ARG cc_start: 0.7966 (mmt180) cc_final: 0.7499 (mpp80) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.2245 time to fit residues: 14.1802 Evaluate side-chains 49 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4983 Z= 0.206 Angle : 0.518 10.747 6747 Z= 0.261 Chirality : 0.041 0.147 737 Planarity : 0.004 0.036 873 Dihedral : 4.815 69.202 660 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.66 % Allowed : 11.05 % Favored : 87.29 % 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: 1.46 (0.37), residues: 594 helix: 1.59 (0.33), residues: 258 sheet: 0.99 (0.61), residues: 85 loop : 0.43 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 581 HIS 0.002 0.000 HIS C 420 PHE 0.008 0.001 PHE C 407 TYR 0.009 0.001 TYR A 127 ARG 0.013 0.001 ARG B 72 *********************** 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 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7789 (mmm) cc_final: 0.7520 (mmm) REVERT: A 140 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8255 (mm-30) REVERT: B 1 MET cc_start: 0.1252 (ptt) cc_final: 0.0492 (ptt) REVERT: B 74 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7479 (mpp80) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.1994 time to fit residues: 13.0543 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4983 Z= 0.201 Angle : 0.517 11.416 6747 Z= 0.260 Chirality : 0.040 0.143 737 Planarity : 0.004 0.035 873 Dihedral : 4.811 69.397 660 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.84 % Allowed : 11.42 % 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: 1.40 (0.37), residues: 594 helix: 1.54 (0.34), residues: 259 sheet: 1.02 (0.61), residues: 84 loop : 0.38 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.002 0.000 HIS C 293 PHE 0.009 0.001 PHE C 522 TYR 0.008 0.001 TYR A 74 ARG 0.012 0.001 ARG A 143 *********************** 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 53 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7783 (mmm) cc_final: 0.7522 (mmm) REVERT: A 140 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 1 MET cc_start: 0.1249 (ptt) cc_final: 0.0478 (ptt) REVERT: B 74 ARG cc_start: 0.7949 (mmt180) cc_final: 0.7496 (mpp80) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.2254 time to fit residues: 14.5752 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.0870 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4983 Z= 0.179 Angle : 0.508 11.685 6747 Z= 0.255 Chirality : 0.040 0.142 737 Planarity : 0.004 0.035 873 Dihedral : 4.794 69.778 660 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.66 % Allowed : 11.42 % Favored : 86.92 % 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: 1.41 (0.37), residues: 594 helix: 1.56 (0.33), residues: 259 sheet: 1.00 (0.61), residues: 84 loop : 0.39 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.002 0.000 HIS A 125 PHE 0.008 0.001 PHE C 522 TYR 0.014 0.001 TYR A 127 ARG 0.016 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 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7772 (mmm) cc_final: 0.7513 (mmm) REVERT: A 140 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8287 (mm-30) REVERT: B 1 MET cc_start: 0.1196 (ptt) cc_final: 0.0450 (ptt) outliers start: 9 outliers final: 9 residues processed: 48 average time/residue: 0.2129 time to fit residues: 13.0096 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4983 Z= 0.223 Angle : 0.534 12.267 6747 Z= 0.267 Chirality : 0.041 0.145 737 Planarity : 0.004 0.035 873 Dihedral : 4.770 68.193 660 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 11.42 % 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: 1.36 (0.37), residues: 594 helix: 1.54 (0.34), residues: 259 sheet: 0.88 (0.61), residues: 85 loop : 0.37 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.002 0.000 HIS C 293 PHE 0.010 0.001 PHE C 522 TYR 0.014 0.001 TYR A 127 ARG 0.012 0.001 ARG A 143 *********************** 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 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7771 (mmm) cc_final: 0.7514 (mmm) REVERT: B 1 MET cc_start: 0.1256 (ptt) cc_final: 0.0518 (ptt) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.2197 time to fit residues: 13.5448 Evaluate side-chains 47 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.4980 chunk 35 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4983 Z= 0.184 Angle : 0.524 12.269 6747 Z= 0.262 Chirality : 0.040 0.141 737 Planarity : 0.004 0.035 873 Dihedral : 4.775 68.710 660 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.66 % Allowed : 11.97 % 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: 1.36 (0.37), residues: 594 helix: 1.52 (0.34), residues: 259 sheet: 0.95 (0.61), residues: 84 loop : 0.36 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 141 HIS 0.002 0.000 HIS A 125 PHE 0.008 0.001 PHE C 522 TYR 0.012 0.001 TYR A 127 ARG 0.012 0.001 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 49 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7759 (mmm) cc_final: 0.7524 (mmm) REVERT: B 1 MET cc_start: 0.1339 (ptt) cc_final: 0.0589 (ptt) outliers start: 9 outliers final: 9 residues processed: 47 average time/residue: 0.2172 time to fit residues: 13.2100 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 TRP Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.127279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083064 restraints weight = 19358.830| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 5.43 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4983 Z= 0.251 Angle : 0.540 12.022 6747 Z= 0.270 Chirality : 0.041 0.146 737 Planarity : 0.004 0.039 873 Dihedral : 4.775 67.536 660 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.66 % Allowed : 11.97 % 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: 1.28 (0.36), residues: 594 helix: 1.45 (0.34), residues: 259 sheet: 0.84 (0.61), residues: 85 loop : 0.37 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.002 0.000 HIS A 125 PHE 0.012 0.001 PHE C 522 TYR 0.014 0.001 TYR A 127 ARG 0.013 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: 1394.84 seconds wall clock time: 25 minutes 17.90 seconds (1517.90 seconds total)