Starting phenix.real_space_refine on Tue Feb 11 08:45:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b55_44200/02_2025/9b55_44200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b55_44200/02_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_44200/02_2025/9b55_44200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b55_44200/02_2025/9b55_44200.map" model { file = "/net/cci-nas-00/data/ceres_data/9b55_44200/02_2025/9b55_44200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b55_44200/02_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-5592/modules/chem_data/mon_lib" Total number of atoms: 4871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 596 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "C" Number of atoms: 3107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} Conformer: "B" Number of residues, atoms: 377, 3099 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} bond proxies already assigned to first conformer: 3161 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.26, per 1000 atoms: 1.08 Number of scatterers: 4871 At special positions: 0 Unit cell: (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: 1.29 Conformation dependent library (CDL) restraints added in 840.9 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, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 98 through 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: 1.23 Time building geometry restraints manager: 1.49 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: 0.010 Normalize map: mean=0, sd=1: 3.570 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.500 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- 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 : 0.605 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: 0.2308 time to fit residues: 17.4371 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 : 0.649 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091562 restraints weight = 10841.056| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.08 r_work: 0.2949 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.078 | | 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) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 83.820 660 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 : 0.567 Fit side-chains REVERT: A 72 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8474 (mtp-110) REVERT: A 112 ASP cc_start: 0.8792 (m-30) cc_final: 0.8419 (m-30) REVERT: A 140 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7868 (mm-30) REVERT: C 351 ARG cc_start: 0.8244 (mtp85) cc_final: 0.8033 (mtp85) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.2248 time to fit residues: 14.7063 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 : 0.572 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 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 = 0.3655 r_free = 0.3655 target = 0.127983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.091405 restraints weight = 8887.827| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.68 r_work: 0.2948 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4983 Z= 0.311 Angle : 0.537 6.593 6747 Z= 0.278 Chirality : 0.043 0.151 737 Planarity : 0.004 0.034 873 Dihedral : 5.518 86.515 660 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.84 % Allowed : 6.81 % Favored : 91.34 % 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: 1.01 (0.35), residues: 594 helix: 1.69 (0.33), residues: 254 sheet: 1.07 (0.59), residues: 78 loop : -0.45 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.003 0.001 HIS C 420 PHE 0.010 0.001 PHE C 407 TYR 0.010 0.001 TYR C 367 ARG 0.004 0.000 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 55 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.555 Fit side-chains REVERT: A 112 ASP cc_start: 0.8863 (m-30) cc_final: 0.8458 (m-30) REVERT: A 140 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 347 LEU cc_start: 0.8450 (tp) cc_final: 0.8163 (tt) REVERT: C 351 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8086 (mtp85) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.2260 time to fit residues: 14.4015 Evaluate side-chains 48 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 0.5980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 19 optimal weight: 0.0770 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.128050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.085180 restraints weight = 13617.519| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.95 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1331 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= 0.165 Angle : 0.468 6.430 6747 Z= 0.245 Chirality : 0.040 0.135 737 Planarity : 0.003 0.035 873 Dihedral : 5.273 79.175 660 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 8.66 % Favored : 90.24 % 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: 1.18 (0.36), residues: 594 helix: 1.82 (0.33), residues: 254 sheet: 1.19 (0.60), residues: 78 loop : -0.36 (0.40), residues: 262 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 428 TYR 0.009 0.001 TYR C 367 ARG 0.002 0.000 ARG A 72 *********************** 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 54 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.618 Fit side-chains REVERT: A 112 ASP cc_start: 0.8670 (m-30) cc_final: 0.8201 (m-30) REVERT: A 140 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7746 (mm-30) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.2255 time to fit residues: 14.9210 Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.125684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.082126 restraints weight = 18152.966| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 5.47 r_work (final): 0.2981 ------------------------------------------------------------------------------- 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1386 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= 0.276 Angle : 0.505 6.851 6747 Z= 0.262 Chirality : 0.042 0.135 737 Planarity : 0.004 0.034 873 Dihedral : 4.834 58.426 660 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.47 % Allowed : 9.02 % Favored : 89.50 % 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: 1.11 (0.36), residues: 594 helix: 1.74 (0.33), residues: 254 sheet: 1.16 (0.58), residues: 83 loop : -0.40 (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 32 PHE 0.010 0.001 PHE C 407 TYR 0.010 0.001 TYR C 367 ARG 0.006 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 49 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8789 (m-30) cc_final: 0.8307 (m-30) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.2123 time to fit residues: 12.6839 Evaluate side-chains 45 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.124020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.084214 restraints weight = 8811.219| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.96 r_work: 0.2801 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4983 Z= 0.339 Angle : 0.536 6.779 6747 Z= 0.279 Chirality : 0.043 0.139 737 Planarity : 0.004 0.034 873 Dihedral : 4.429 30.274 660 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.84 % Allowed : 8.84 % 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: 0.96 (0.36), residues: 594 helix: 1.60 (0.33), residues: 254 sheet: 1.13 (0.59), residues: 83 loop : -0.47 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 581 HIS 0.002 0.001 HIS A 75 PHE 0.012 0.001 PHE C 407 TYR 0.010 0.001 TYR C 367 ARG 0.007 0.001 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 50 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8793 (m-30) cc_final: 0.8275 (m-30) REVERT: A 140 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7897 (mm-30) REVERT: C 347 LEU cc_start: 0.8214 (tp) cc_final: 0.7989 (tt) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.2118 time to fit residues: 12.8562 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 : 0.593 ------------------------------------------------------------------------------- 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 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 42 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.126000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.082425 restraints weight = 18106.833| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 5.48 r_work (final): 0.2980 ------------------------------------------------------------------------------- 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 = 0.47 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: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4983 Z= 0.217 Angle : 0.492 7.301 6747 Z= 0.254 Chirality : 0.041 0.134 737 Planarity : 0.004 0.036 873 Dihedral : 4.459 30.853 660 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.47 % Allowed : 9.02 % Favored : 89.50 % 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: 1.73 (0.33), residues: 254 sheet: 1.32 (0.59), residues: 82 loop : -0.43 (0.41), residues: 258 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 0.004 0.000 ARG C 351 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8650 (m-30) cc_final: 0.8141 (m-30) REVERT: C 294 MET cc_start: 0.4435 (tpp) cc_final: 0.4032 (tpp) REVERT: C 347 LEU cc_start: 0.8224 (tp) cc_final: 0.8007 (tt) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.2014 time to fit residues: 12.7008 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 : 0.560 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.125515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.085090 restraints weight = 10762.476| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.68 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4983 Z= 0.246 Angle : 0.497 6.856 6747 Z= 0.257 Chirality : 0.042 0.136 737 Planarity : 0.004 0.035 873 Dihedral : 4.486 36.080 660 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.47 % Allowed : 9.58 % Favored : 88.95 % 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: 1.06 (0.36), residues: 594 helix: 1.69 (0.33), residues: 254 sheet: 1.29 (0.60), residues: 82 loop : -0.46 (0.41), residues: 258 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 407 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 51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.601 Fit side-chains REVERT: A 112 ASP cc_start: 0.8552 (m-30) cc_final: 0.8022 (m-30) REVERT: C 294 MET cc_start: 0.4338 (tpp) cc_final: 0.3922 (tpp) REVERT: C 347 LEU cc_start: 0.8119 (tp) cc_final: 0.7888 (tt) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 0.2001 time to fit residues: 12.2076 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 : 0.609 ------------------------------------------------------------------------------- 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: 0.5980 chunk 45 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 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 = 0.3530 r_free = 0.3530 target = 0.123784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.084107 restraints weight = 10713.649| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.24 r_work: 0.2800 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1577 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= 0.249 Angle : 0.495 6.667 6747 Z= 0.257 Chirality : 0.041 0.134 737 Planarity : 0.004 0.035 873 Dihedral : 4.416 34.520 660 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 9.76 % Favored : 88.58 % 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: 1.27 (0.60), residues: 82 loop : -0.46 (0.41), residues: 258 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 407 TYR 0.010 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 52 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8713 (m-30) cc_final: 0.8204 (m-30) REVERT: A 140 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7747 (mm-30) REVERT: C 294 MET cc_start: 0.4487 (tpp) cc_final: 0.4111 (tpp) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.2096 time to fit residues: 12.8143 Evaluate side-chains 51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 425 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.126203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.085765 restraints weight = 9146.709| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.10 r_work: 0.2814 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4983 Z= 0.223 Angle : 0.495 6.595 6747 Z= 0.257 Chirality : 0.042 0.142 737 Planarity : 0.003 0.035 873 Dihedral : 4.406 34.231 660 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.29 % Allowed : 10.31 % 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: 1.10 (0.36), residues: 594 helix: 1.74 (0.33), residues: 254 sheet: 1.27 (0.59), residues: 82 loop : -0.45 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS C 420 PHE 0.009 0.001 PHE C 522 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 53 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8699 (m-30) cc_final: 0.8186 (m-30) REVERT: A 114 ASN cc_start: 0.8951 (t0) cc_final: 0.8578 (t0) REVERT: A 140 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7741 (mm-30) REVERT: C 294 MET cc_start: 0.4509 (tpp) cc_final: 0.4133 (tpp) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.2110 time to fit residues: 13.1654 Evaluate side-chains 51 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 36 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain C residue 425 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 22 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.126197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083313 restraints weight = 14984.117| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 5.08 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4983 Z= 0.222 Angle : 0.497 6.440 6747 Z= 0.260 Chirality : 0.041 0.135 737 Planarity : 0.003 0.035 873 Dihedral : 4.402 34.524 660 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.66 % Allowed : 10.31 % 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: 1.11 (0.36), residues: 594 helix: 1.76 (0.33), residues: 254 sheet: 1.29 (0.60), residues: 82 loop : -0.46 (0.41), residues: 258 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 0.009 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: 2502.31 seconds wall clock time: 44 minutes 58.53 seconds (2698.53 seconds total)