Starting phenix.real_space_refine on Thu Mar 6 04:31:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b56_44201/03_2025/9b56_44201.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b56_44201/03_2025/9b56_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/cci-nas-00/data/ceres_data/9b56_44201/03_2025/9b56_44201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b56_44201/03_2025/9b56_44201.map" model { file = "/net/cci-nas-00/data/ceres_data/9b56_44201/03_2025/9b56_44201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b56_44201/03_2025/9b56_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.46, per 1000 atoms: 1.12 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 - 3.00 Amino acid : True - 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: 1.34 Conformation dependent library (CDL) restraints added in 926.9 milliseconds 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: 0.65 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: 1.35 Time building geometry restraints manager: 1.55 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: 0.00 - 0.80: 6309 0.80 - 1.59: 366 1.59 - 2.39: 32 2.39 - 3.19: 16 3.19 - 3.98: 24 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: 2.620 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.660 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.596 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: 0.2100 time to fit residues: 23.0814 Evaluate side-chains 59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.147039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112313 restraints weight = 11719.114| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.75 r_work: 0.3290 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: B 18 GLU cc_start: 0.8635 (tp30) cc_final: 0.8391 (tp30) REVERT: C 568 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7973 (mtt90) REVERT: C 613 MET cc_start: 0.8984 (ttt) cc_final: 0.8676 (ttt) REVERT: C 632 GLN cc_start: 0.8480 (mt0) cc_final: 0.8261 (mt0) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.2250 time to fit residues: 17.6363 Evaluate side-chains 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.145477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110524 restraints weight = 9637.857| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.77 r_work: 0.3329 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1759 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= 0.282 Angle : 0.537 5.632 6747 Z= 0.278 Chirality : 0.043 0.218 737 Planarity : 0.004 0.035 873 Dihedral : 5.450 46.401 668 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.66 % Allowed : 12.52 % Favored : 85.82 % 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: 1.14 (0.36), residues: 594 helix: 1.47 (0.33), residues: 257 sheet: 1.18 (0.60), residues: 85 loop : -0.05 (0.41), residues: 252 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 0.021 0.002 PHE B 45 TYR 0.013 0.001 TYR C 419 ARG 0.003 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 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 568 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7972 (mtt90) REVERT: C 613 MET cc_start: 0.8995 (ttt) cc_final: 0.8720 (ttt) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.2155 time to fit residues: 15.6208 Evaluate side-chains 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 413 VAL 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 12 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.2774 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.148293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112880 restraints weight = 15061.525| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.61 r_work: 0.3268 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4983 Z= 0.148 Angle : 0.496 8.124 6747 Z= 0.253 Chirality : 0.041 0.165 737 Planarity : 0.004 0.035 873 Dihedral : 5.012 46.383 666 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.39 % Allowed : 12.15 % 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: 1.27 (0.36), residues: 594 helix: 1.60 (0.33), residues: 256 sheet: 1.48 (0.61), residues: 81 loop : -0.07 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.002 0.000 HIS C 371 PHE 0.023 0.001 PHE B 45 TYR 0.008 0.001 TYR C 419 ARG 0.010 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 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: C 568 ARG cc_start: 0.8323 (mtt180) cc_final: 0.8080 (mtt90) REVERT: C 613 MET cc_start: 0.9048 (ttt) cc_final: 0.8743 (ttt) outliers start: 13 outliers final: 8 residues processed: 59 average time/residue: 0.2501 time to fit residues: 19.9327 Evaluate side-chains 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 466 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.146109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111836 restraints weight = 20001.824| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 6.28 r_work: 0.3150 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2003 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= 0.241 Angle : 0.538 8.676 6747 Z= 0.270 Chirality : 0.042 0.166 737 Planarity : 0.004 0.035 873 Dihedral : 5.055 46.259 666 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.21 % Allowed : 13.08 % 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: 1.21 (0.36), residues: 594 helix: 1.62 (0.33), residues: 255 sheet: 1.33 (0.61), residues: 83 loop : -0.17 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.001 HIS C 420 PHE 0.012 0.001 PHE B 45 TYR 0.015 0.001 TYR A 74 ARG 0.003 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 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7912 (tp) REVERT: A 143 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7699 (ttp80) REVERT: C 568 ARG cc_start: 0.8446 (mtt180) cc_final: 0.8161 (mtt90) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.2138 time to fit residues: 15.8909 Evaluate side-chains 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.147279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110714 restraints weight = 9694.286| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.35 r_work: 0.3313 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2086 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= 0.206 Angle : 0.523 7.629 6747 Z= 0.264 Chirality : 0.041 0.149 737 Planarity : 0.004 0.035 873 Dihedral : 5.001 46.515 666 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.03 % Allowed : 13.26 % 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: 1.24 (0.36), residues: 594 helix: 1.62 (0.33), residues: 256 sheet: 1.43 (0.61), residues: 81 loop : -0.14 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 581 HIS 0.001 0.001 HIS C 420 PHE 0.010 0.001 PHE C 640 TYR 0.014 0.001 TYR A 74 ARG 0.003 0.000 ARG B 54 *********************** 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 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7762 (tp) REVERT: C 568 ARG cc_start: 0.8246 (mtt180) cc_final: 0.8043 (mtt90) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.1898 time to fit residues: 14.3439 Evaluate side-chains 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 347 LEU Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 466 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112055 restraints weight = 20065.658| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 6.66 r_work: 0.3141 rms_B_bonded: 5.94 restraints_weight: 2.0000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4983 Z= 0.205 Angle : 0.522 7.726 6747 Z= 0.264 Chirality : 0.041 0.149 737 Planarity : 0.004 0.035 873 Dihedral : 4.945 46.379 666 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.21 % Allowed : 13.44 % Favored : 84.35 % 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: 1.23 (0.36), residues: 594 helix: 1.62 (0.33), residues: 256 sheet: 1.46 (0.61), residues: 81 loop : -0.16 (0.41), residues: 257 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 0.014 0.001 PHE C 640 TYR 0.013 0.001 TYR A 74 ARG 0.008 0.000 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 59 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7928 (tp) REVERT: C 568 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8163 (mtt90) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.1882 time to fit residues: 13.3704 Evaluate side-chains 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 413 VAL 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 40 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.0470 chunk 26 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.146178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112999 restraints weight = 11826.126| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.53 r_work: 0.3334 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2240 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= 0.149 Angle : 0.530 8.977 6747 Z= 0.266 Chirality : 0.042 0.192 737 Planarity : 0.004 0.035 873 Dihedral : 4.835 46.191 666 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.47 % Allowed : 14.36 % 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: 1.34 (0.36), residues: 594 helix: 1.71 (0.33), residues: 256 sheet: 1.52 (0.61), residues: 81 loop : -0.12 (0.41), residues: 257 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 0.011 0.001 PHE B 45 TYR 0.013 0.001 TYR A 74 ARG 0.009 0.000 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 56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7714 (ttp-110) outliers start: 8 outliers final: 8 residues processed: 53 average time/residue: 0.1896 time to fit residues: 12.9821 Evaluate side-chains 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 466 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.146938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113195 restraints weight = 12007.835| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.59 r_work: 0.3303 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4983 Z= 0.223 Angle : 0.546 9.335 6747 Z= 0.275 Chirality : 0.042 0.165 737 Planarity : 0.004 0.034 873 Dihedral : 4.905 46.226 666 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.84 % Allowed : 14.00 % 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: 1.66 (0.33), residues: 256 sheet: 1.35 (0.60), residues: 81 loop : -0.16 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.001 0.000 HIS C 420 PHE 0.011 0.001 PHE B 45 TYR 0.013 0.001 TYR A 74 ARG 0.010 0.000 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 56 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 LYS cc_start: 0.4936 (pttp) cc_final: 0.4494 (pttp) outliers start: 10 outliers final: 9 residues processed: 53 average time/residue: 0.1776 time to fit residues: 12.4177 Evaluate side-chains 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 C residue 347 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.146877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112466 restraints weight = 10213.527| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.45 r_work: 0.3320 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2312 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= 0.197 Angle : 0.549 9.589 6747 Z= 0.276 Chirality : 0.042 0.153 737 Planarity : 0.004 0.034 873 Dihedral : 4.908 46.238 666 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 14.73 % Favored : 83.61 % 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: 1.26 (0.36), residues: 594 helix: 1.69 (0.34), residues: 256 sheet: 1.32 (0.60), residues: 81 loop : -0.15 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 581 HIS 0.002 0.001 HIS B 68 PHE 0.011 0.001 PHE B 45 TYR 0.012 0.001 TYR A 74 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 58 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7751 (tp) REVERT: C 304 MET cc_start: 0.8647 (ttp) cc_final: 0.7928 (ttt) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.2431 time to fit residues: 17.7794 Evaluate side-chains 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.145705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111053 restraints weight = 16441.250| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.81 r_work: 0.3247 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4983 Z= 0.163 Angle : 0.542 9.087 6747 Z= 0.275 Chirality : 0.041 0.164 737 Planarity : 0.004 0.034 873 Dihedral : 4.823 46.121 666 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: 1.33 (0.36), residues: 594 helix: 1.77 (0.34), residues: 256 sheet: 1.31 (0.61), residues: 81 loop : -0.12 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 581 HIS 0.002 0.001 HIS C 371 PHE 0.012 0.001 PHE C 640 TYR 0.012 0.001 TYR A 74 ARG 0.010 0.000 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: 3012.71 seconds wall clock time: 54 minutes 3.97 seconds (3243.97 seconds total)