Starting phenix.real_space_refine on Thu Mar 6 04:34:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b55_44200/03_2025/9b55_44200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b55_44200/03_2025/9b55_44200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b55_44200/03_2025/9b55_44200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b55_44200/03_2025/9b55_44200.map" model { file = "/net/cci-nas-00/data/ceres_data/9b55_44200/03_2025/9b55_44200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b55_44200/03_2025/9b55_44200.cif" } resolution = 3.23 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= 0.053 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. Time to flip 3 residue(s): 0.01s 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: 5.19, per 1000 atoms: 1.07 Number of scatterers: 4871 At special positions: 0 Unit cell: (59.584, 81.928, 105.336, 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: 1.22 Conformation dependent library (CDL) restraints added in 867.4 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, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.999A 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 56 through 60 Processing helix chain 'C' and resid 293 through 306 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: 3.585A pdb=" N SER C 398 " --> pdb=" O PRO C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 removed outlier: 4.332A pdb=" N TYR C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.753A 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: 3.840A 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: 3.713A 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 531 Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.649A pdb=" N LEU C 538 " --> pdb=" O PRO C 534 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 534 through 539' 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: 3.948A pdb=" N PHE C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 601 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 662 removed outlier: 3.706A pdb=" N ILE C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) 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: 4.145A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 321 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 474 through 479 removed outlier: 3.734A 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 568 222 hydrogen bonds defined for protein. 623 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: 1.33 Time building geometry restraints manager: 1.45 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: 1241 1.41 - 1.54: 2896 1.54 - 1.68: 2 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 1.525 -0.072 2.00e-02 2.50e+03 1.30e+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 3.08e+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 2.79e+00 bond pdb=" C05 A1AIV B 101 " pdb=" N06 A1AIV B 101 " ideal model delta sigma weight residual 1.151 1.131 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CA VAL A 120 " pdb=" CB VAL A 120 " ideal model delta sigma weight residual 1.540 1.534 0.006 9.00e-03 1.23e+04 4.25e-01 ... (remaining 4978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 6451 1.00 - 2.00: 228 2.00 - 3.00: 34 3.00 - 4.00: 33 4.00 - 5.00: 1 Bond angle restraints: 6747 Sorted by residual: angle pdb=" N LEU A 89 " pdb=" CA LEU A 89 " pdb=" C LEU A 89 " ideal model delta sigma weight residual 108.24 105.14 3.10 1.32e+00 5.74e-01 5.51e+00 angle pdb=" C ILE A 88 " pdb=" N LEU A 89 " pdb=" CA LEU A 89 " ideal model delta sigma weight residual 122.32 125.55 -3.23 1.76e+00 3.23e-01 3.36e+00 angle pdb=" N ILE A 88 " pdb=" CA ILE A 88 " pdb=" C ILE A 88 " ideal model delta sigma weight residual 111.58 109.70 1.88 1.06e+00 8.90e-01 3.16e+00 angle pdb=" CA VAL A 120 " pdb=" C VAL A 120 " pdb=" O VAL A 120 " ideal model delta sigma weight residual 120.88 119.68 1.20 6.80e-01 2.16e+00 3.12e+00 angle pdb=" N HIS B 68 " pdb=" CA HIS B 68 " pdb=" C HIS B 68 " ideal model delta sigma weight residual 108.90 111.76 -2.86 1.63e+00 3.76e-01 3.07e+00 ... (remaining 6742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 2769 13.01 - 26.02: 199 26.02 - 39.03: 38 39.03 - 52.04: 11 52.04 - 65.05: 1 Dihedral angle restraints: 3018 sinusoidal: 1254 harmonic: 1764 Sorted by residual: dihedral pdb=" CA ASP A 87 " pdb=" C ASP A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LEU B 69 " pdb=" C LEU B 69 " pdb=" N VAL B 70 " pdb=" CA VAL B 70 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+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 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 438 0.028 - 0.056: 205 0.056 - 0.084: 49 0.084 - 0.112: 30 0.112 - 0.140: 15 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ILE B 36 " pdb=" N ILE B 36 " pdb=" C ILE B 36 " pdb=" CB ILE B 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 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 4.67e-01 chirality pdb=" CA ILE C 645 " pdb=" N ILE C 645 " pdb=" C ILE C 645 " pdb=" CB ILE C 645 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 734 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 67 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU B 67 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU B 67 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS B 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.08e-01 pdb=" N PRO A 76 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 5 " -0.005 2.00e-02 2.50e+03 9.50e-03 9.02e-01 pdb=" C VAL B 5 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL B 5 " -0.006 2.00e-02 2.50e+03 pdb=" N LYS B 6 " -0.006 2.00e-02 2.50e+03 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 11 2.45 - 3.06: 3323 3.06 - 3.67: 6653 3.67 - 4.29: 10184 4.29 - 4.90: 17785 Nonbonded interactions: 37956 Sorted by model distance: nonbonded pdb=" SG CYS A 85 " pdb=" C03 A1AIV B 101 " model vdw 1.834 3.800 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 29 " model vdw 2.222 3.120 nonbonded pdb=" OD1 ASP C 555 " pdb=" N ILE C 556 " model vdw 2.240 3.120 nonbonded pdb=" N GLU C 664 " pdb=" OE1 GLU C 664 " model vdw 2.300 3.120 nonbonded pdb=" OG SER C 608 " pdb=" OD2 ASP C 612 " model vdw 2.304 3.040 ... (remaining 37951 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.020 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4983 Z= 0.275 Angle : 0.505 5.004 6747 Z= 0.274 Chirality : 0.040 0.140 737 Planarity : 0.003 0.024 873 Dihedral : 9.785 65.045 1878 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % 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: 0.82 (0.35), residues: 594 helix: 1.85 (0.35), residues: 242 sheet: 0.58 (0.57), residues: 80 loop : -0.66 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 581 HIS 0.003 0.001 HIS A 75 PHE 0.009 0.001 PHE C 407 TYR 0.008 0.001 TYR C 453 ARG 0.001 0.000 ARG B 42 *********************** 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 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8718 (m-30) cc_final: 0.8390 (m-30) REVERT: A 114 ASN cc_start: 0.8851 (t0) cc_final: 0.8519 (t0) REVERT: C 347 LEU cc_start: 0.8753 (tp) cc_final: 0.8488 (tt) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2226 time to fit residues: 16.7497 Evaluate side-chains 43 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.129474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091557 restraints weight = 10841.097| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.08 r_work: 0.2951 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1020 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= 0.209 Angle : 0.527 5.960 6747 Z= 0.273 Chirality : 0.042 0.144 737 Planarity : 0.004 0.032 873 Dihedral : 5.405 83.821 660 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.10 % Allowed : 7.00 % Favored : 91.90 % 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: 1.22 (0.35), residues: 594 helix: 1.94 (0.34), residues: 245 sheet: 1.05 (0.58), residues: 78 loop : -0.30 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS A 32 PHE 0.010 0.001 PHE C 428 TYR 0.013 0.001 TYR A 145 ARG 0.003 0.000 ARG C 351 *********************** 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 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.544 Fit side-chains REVERT: A 72 ARG cc_start: 0.8696 (mtp-110) cc_final: 0.8470 (mtp-110) REVERT: A 112 ASP cc_start: 0.8789 (m-30) cc_final: 0.8416 (m-30) REVERT: A 140 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 351 ARG cc_start: 0.8247 (mtp85) cc_final: 0.8037 (mtp85) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.3013 time to fit residues: 19.8330 Evaluate side-chains 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.124076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.084066 restraints weight = 8763.970| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.97 r_work: 0.2798 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4983 Z= 0.385 Angle : 0.572 6.408 6747 Z= 0.297 Chirality : 0.044 0.151 737 Planarity : 0.004 0.034 873 Dihedral : 5.383 77.079 660 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.84 % Allowed : 7.18 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.35), residues: 594 helix: 1.56 (0.33), residues: 254 sheet: 1.00 (0.59), residues: 78 loop : -0.48 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.003 0.001 HIS A 75 PHE 0.011 0.002 PHE C 407 TYR 0.012 0.001 TYR C 453 ARG 0.004 0.001 ARG C 412 *********************** 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 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 1.433 Fit side-chains REVERT: A 112 ASP cc_start: 0.8842 (m-30) cc_final: 0.8399 (m-30) REVERT: A 140 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8028 (mm-30) REVERT: C 347 LEU cc_start: 0.8327 (tp) cc_final: 0.8033 (tt) REVERT: C 351 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7987 (mtp85) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.4511 time to fit residues: 29.4881 Evaluate side-chains 47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 318 GLN Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.126728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.083890 restraints weight = 13671.347| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.94 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1329 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= 0.203 Angle : 0.483 6.266 6747 Z= 0.252 Chirality : 0.041 0.139 737 Planarity : 0.004 0.036 873 Dihedral : 5.038 66.684 660 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.10 % Allowed : 9.02 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.08 (0.36), residues: 594 helix: 1.70 (0.33), residues: 254 sheet: 1.17 (0.61), residues: 78 loop : -0.37 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.002 0.001 HIS C 420 PHE 0.008 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.002 0.000 ARG C 563 *********************** 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 51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.818 Fit side-chains REVERT: A 112 ASP cc_start: 0.8677 (m-30) cc_final: 0.8173 (m-30) REVERT: A 140 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7712 (mm-30) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.3638 time to fit residues: 23.7602 Evaluate side-chains 46 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.125890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.082168 restraints weight = 18138.834| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 5.50 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4983 Z= 0.252 Angle : 0.502 6.584 6747 Z= 0.259 Chirality : 0.042 0.137 737 Planarity : 0.004 0.035 873 Dihedral : 4.634 41.313 660 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.84 % Allowed : 9.02 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.07 (0.36), residues: 594 helix: 1.70 (0.33), residues: 254 sheet: 1.20 (0.59), residues: 83 loop : -0.44 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS A 75 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.007 0.000 ARG A 72 *********************** 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 to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8759 (m-30) cc_final: 0.8238 (m-30) REVERT: A 140 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7662 (mm-30) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.2834 time to fit residues: 17.3413 Evaluate side-chains 47 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 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 = 0.3555 r_free = 0.3555 target = 0.125754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.085614 restraints weight = 8768.185| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.99 r_work: 0.2819 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4983 Z= 0.263 Angle : 0.497 7.006 6747 Z= 0.257 Chirality : 0.042 0.137 737 Planarity : 0.004 0.036 873 Dihedral : 4.497 30.912 660 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.21 % Allowed : 8.47 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.07 (0.36), residues: 594 helix: 1.70 (0.33), residues: 254 sheet: 1.19 (0.59), residues: 83 loop : -0.44 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS C 420 PHE 0.009 0.001 PHE C 407 TYR 0.009 0.001 TYR C 367 ARG 0.007 0.000 ARG A 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 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8804 (m-30) cc_final: 0.8282 (m-30) outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.1880 time to fit residues: 12.4978 Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 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 = 0.3566 r_free = 0.3566 target = 0.126659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.082542 restraints weight = 18090.255| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 5.54 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1505 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= 0.222 Angle : 0.486 7.492 6747 Z= 0.251 Chirality : 0.041 0.143 737 Planarity : 0.004 0.036 873 Dihedral : 4.393 31.231 660 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.10 % Allowed : 10.13 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.12 (0.36), residues: 594 helix: 1.74 (0.33), residues: 254 sheet: 1.23 (0.59), residues: 83 loop : -0.41 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS A 75 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.007 0.000 ARG A 72 *********************** 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 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.528 Fit side-chains REVERT: A 112 ASP cc_start: 0.8677 (m-30) cc_final: 0.8123 (m-30) REVERT: A 140 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7506 (mm-30) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.2253 time to fit residues: 13.3013 Evaluate side-chains 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.126608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.085178 restraints weight = 10758.435| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.42 r_work: 0.2800 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1533 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= 0.202 Angle : 0.477 7.651 6747 Z= 0.247 Chirality : 0.041 0.134 737 Planarity : 0.003 0.036 873 Dihedral : 4.313 31.234 660 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.47 % Allowed : 10.13 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.15 (0.36), residues: 594 helix: 1.76 (0.33), residues: 254 sheet: 1.26 (0.59), residues: 83 loop : -0.40 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.004 0.000 ARG C 351 *********************** 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 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8711 (m-30) cc_final: 0.8201 (m-30) REVERT: A 140 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7746 (mm-30) REVERT: C 294 MET cc_start: 0.4358 (tpp) cc_final: 0.3951 (tpp) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.2084 time to fit residues: 12.8685 Evaluate side-chains 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 389 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 14 optimal weight: 0.0870 chunk 25 optimal weight: 0.0670 chunk 9 optimal weight: 0.0060 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.1312 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.129379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.087857 restraints weight = 10623.010| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.44 r_work: 0.2838 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4983 Z= 0.122 Angle : 0.453 7.282 6747 Z= 0.236 Chirality : 0.040 0.136 737 Planarity : 0.003 0.038 873 Dihedral : 4.209 32.772 660 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.29 % Allowed : 11.23 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.94 (0.34), residues: 254 sheet: 1.25 (0.58), residues: 83 loop : -0.28 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.001 0.000 HIS A 32 PHE 0.010 0.001 PHE C 428 TYR 0.008 0.001 TYR C 367 ARG 0.004 0.000 ARG C 351 *********************** 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 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8579 (m-30) cc_final: 0.8080 (m-30) REVERT: A 114 ASN cc_start: 0.8923 (t0) cc_final: 0.8568 (t0) REVERT: A 140 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7799 (mm-30) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.1987 time to fit residues: 14.1006 Evaluate side-chains 50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.125470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.085361 restraints weight = 9177.485| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.07 r_work: 0.2811 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4983 Z= 0.290 Angle : 0.514 8.524 6747 Z= 0.263 Chirality : 0.042 0.145 737 Planarity : 0.004 0.035 873 Dihedral : 4.319 31.477 660 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.74 % Allowed : 11.05 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.16 (0.36), residues: 594 helix: 1.83 (0.33), residues: 254 sheet: 1.28 (0.59), residues: 82 loop : -0.46 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 581 HIS 0.002 0.001 HIS A 75 PHE 0.011 0.001 PHE C 407 TYR 0.010 0.001 TYR C 367 ARG 0.004 0.000 ARG C 351 ********************** 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 to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8522 (mtp-110) cc_final: 0.8217 (mtp85) REVERT: A 112 ASP cc_start: 0.8724 (m-30) cc_final: 0.8204 (m-30) REVERT: A 140 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7799 (mm-30) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.2273 time to fit residues: 13.7907 Evaluate side-chains 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 23 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.127212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.084074 restraints weight = 14961.124| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 5.12 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1657 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= 0.188 Angle : 0.480 8.393 6747 Z= 0.246 Chirality : 0.040 0.132 737 Planarity : 0.004 0.036 873 Dihedral : 4.239 31.406 660 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.74 % Allowed : 11.23 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.86 (0.33), residues: 254 sheet: 1.29 (0.59), residues: 82 loop : -0.43 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.000 HIS C 420 PHE 0.009 0.001 PHE C 522 TYR 0.009 0.001 TYR C 367 ARG 0.004 0.000 ARG C 351 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2847.10 seconds wall clock time: 51 minutes 19.11 seconds (3079.11 seconds total)