Starting phenix.real_space_refine on Thu Jul 24 15:07:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfe_45543/07_2025/9cfe_45543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfe_45543/07_2025/9cfe_45543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfe_45543/07_2025/9cfe_45543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfe_45543/07_2025/9cfe_45543.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfe_45543/07_2025/9cfe_45543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfe_45543/07_2025/9cfe_45543.cif" } resolution = 3.03 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= 0.023 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2064 2.51 5 N 550 2.21 5 O 624 1.98 5 H 3130 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6382 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1750 Classifications: {'peptide': 115} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "B" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1655 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2977 Classifications: {'peptide': 193} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 181} Time building chain proxies: 4.43, per 1000 atoms: 0.69 Number of scatterers: 6382 At special positions: 0 Unit cell: (72.21, 62.25, 98.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 624 8.00 N 550 7.00 C 2064 6.00 H 3130 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 623.6 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 7 sheets defined 13.7% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.604A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.865A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.530A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLY A 10 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLY A 10 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.465A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.054A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 119 hydrogen bonds defined for protein. 279 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: 2.28 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 3126 1.11 - 1.29: 530 1.29 - 1.47: 1268 1.47 - 1.65: 1524 1.65 - 1.83: 16 Bond restraints: 6464 Sorted by residual: bond pdb=" N TYR B 36 " pdb=" H TYR B 36 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" CZ PHE C 374 " pdb=" HZ PHE C 374 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CD1 PHE B 99 " pdb=" HD1 PHE B 99 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N GLU B 17 " pdb=" H GLU B 17 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLY A 106 " pdb=" H GLY A 106 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 6459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 9521 2.46 - 4.92: 1593 4.92 - 7.38: 434 7.38 - 9.83: 48 9.83 - 12.29: 4 Bond angle restraints: 11600 Sorted by residual: angle pdb=" CA PHE A 67 " pdb=" CB PHE A 67 " pdb=" CG PHE A 67 " ideal model delta sigma weight residual 113.80 120.42 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" CA PRO C 521 " pdb=" N PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 112.00 102.92 9.08 1.40e+00 5.10e-01 4.20e+01 angle pdb=" CA ASN C 360 " pdb=" CB ASN C 360 " pdb=" CG ASN C 360 " ideal model delta sigma weight residual 112.60 118.79 -6.19 1.00e+00 1.00e+00 3.84e+01 angle pdb=" CA ILE A 12 " pdb=" CB ILE A 12 " pdb=" CG1 ILE A 12 " ideal model delta sigma weight residual 110.40 120.16 -9.76 1.70e+00 3.46e-01 3.29e+01 angle pdb=" OD1 ASN C 360 " pdb=" CG ASN C 360 " pdb=" ND2 ASN C 360 " ideal model delta sigma weight residual 122.60 116.91 5.69 1.00e+00 1.00e+00 3.24e+01 ... (remaining 11595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 2733 15.62 - 31.24: 232 31.24 - 46.86: 81 46.86 - 62.48: 47 62.48 - 78.10: 11 Dihedral angle restraints: 3104 sinusoidal: 1652 harmonic: 1452 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -158.64 72.64 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" C PRO C 521 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " pdb=" CB PRO C 521 " ideal model delta harmonic sigma weight residual -120.70 -139.31 18.61 0 2.50e+00 1.60e-01 5.54e+01 dihedral pdb=" N PRO C 521 " pdb=" C PRO C 521 " pdb=" CA PRO C 521 " pdb=" CB PRO C 521 " ideal model delta harmonic sigma weight residual 115.10 133.13 -18.03 0 2.50e+00 1.60e-01 5.20e+01 ... (remaining 3101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 438 0.176 - 0.351: 43 0.351 - 0.526: 2 0.526 - 0.702: 0 0.702 - 0.877: 2 Chirality restraints: 485 Sorted by residual: chirality pdb=" CA PRO C 521 " pdb=" N PRO C 521 " pdb=" C PRO C 521 " pdb=" CB PRO C 521 " both_signs ideal model delta sigma weight residual False 2.72 1.84 0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" CA HIS C 519 " pdb=" N HIS C 519 " pdb=" C HIS C 519 " pdb=" CB HIS C 519 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA ASN C 501 " pdb=" N ASN C 501 " pdb=" C ASN C 501 " pdb=" CB ASN C 501 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 482 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " 0.321 2.00e-02 2.50e+03 1.22e-01 5.92e+02 pdb=" CG TRP A 47 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " -0.112 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " -0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " -0.119 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " 0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " -0.065 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " 0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP A 47 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP A 47 " -0.141 2.00e-02 2.50e+03 pdb=" HE3 TRP A 47 " -0.152 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 47 " 0.120 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 47 " -0.056 2.00e-02 2.50e+03 pdb=" HH2 TRP A 47 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 97 " 0.051 9.50e-02 1.11e+02 1.35e-01 4.01e+02 pdb=" NE ARG A 97 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 97 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 97 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 97 " 0.040 2.00e-02 2.50e+03 pdb="HH11 ARG A 97 " -0.094 2.00e-02 2.50e+03 pdb="HH12 ARG A 97 " 0.252 2.00e-02 2.50e+03 pdb="HH21 ARG A 97 " 0.133 2.00e-02 2.50e+03 pdb="HH22 ARG A 97 " -0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 403 " -0.772 9.50e-02 1.11e+02 2.77e-01 3.02e+02 pdb=" NE ARG C 403 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C 403 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG C 403 " -0.131 2.00e-02 2.50e+03 pdb=" NH2 ARG C 403 " 0.058 2.00e-02 2.50e+03 pdb="HH11 ARG C 403 " 0.218 2.00e-02 2.50e+03 pdb="HH12 ARG C 403 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG C 403 " 0.113 2.00e-02 2.50e+03 pdb="HH22 ARG C 403 " -0.074 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 434 2.18 - 2.78: 10951 2.78 - 3.39: 17813 3.39 - 3.99: 24523 3.99 - 4.60: 35321 Nonbonded interactions: 89042 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" HG SER C 366 " model vdw 1.570 2.450 nonbonded pdb=" OD1 ASP A 72 " pdb=" HG SER A 74 " model vdw 1.597 2.450 nonbonded pdb=" HG SER A 25 " pdb=" OE1 GLU A 26 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU B 90 " pdb=" HG SER B 92 " model vdw 1.607 2.450 nonbonded pdb="HG13 ILE A 12 " pdb=" H GLN A 13 " model vdw 1.614 2.270 ... (remaining 89037 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=1.00 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: 3.490 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.960 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:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 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 : 0.013 0.057 3338 Z= 0.790 Angle : 1.935 9.757 4540 Z= 1.272 Chirality : 0.117 0.877 485 Planarity : 0.018 0.245 592 Dihedral : 13.560 78.098 1196 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.98 % Allowed : 6.83 % Favored : 92.20 % Rotamer: Outliers : 1.98 % Allowed : 7.34 % Favored : 90.68 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 9.09 % 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: -1.68 (0.37), residues: 410 helix: -4.09 (0.41), residues: 41 sheet: 0.18 (0.48), residues: 110 loop : -1.22 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.196 0.028 TRP A 47 HIS 0.010 0.006 HIS C 519 PHE 0.054 0.013 PHE C 342 TYR 0.204 0.024 TYR C 421 ARG 0.013 0.002 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.14160 ( 115) hydrogen bonds : angle 9.24095 ( 279) SS BOND : bond 0.01259 ( 4) SS BOND : angle 3.99635 ( 8) covalent geometry : bond 0.01322 ( 3334) covalent geometry : angle 1.92934 ( 4532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7473 (t80) REVERT: C 393 THR cc_start: 0.6198 (OUTLIER) cc_final: 0.5809 (m) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.4147 time to fit residues: 44.5255 Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 521 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 493 GLN C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.119532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.110781 restraints weight = 33391.301| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 4.77 r_work: 0.3811 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3338 Z= 0.175 Angle : 0.715 7.214 4540 Z= 0.380 Chirality : 0.047 0.255 485 Planarity : 0.007 0.107 592 Dihedral : 8.726 70.048 474 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.12 % Favored : 94.39 % Rotamer: Outliers : 1.41 % Allowed : 15.54 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.38), residues: 410 helix: -3.44 (0.64), residues: 28 sheet: -0.40 (0.43), residues: 140 loop : -0.98 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 94 HIS 0.002 0.001 HIS C 519 PHE 0.008 0.001 PHE C 486 TYR 0.024 0.002 TYR C 369 ARG 0.008 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 115) hydrogen bonds : angle 7.13166 ( 279) SS BOND : bond 0.00547 ( 4) SS BOND : angle 1.62214 ( 8) covalent geometry : bond 0.00418 ( 3334) covalent geometry : angle 0.71243 ( 4532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7933 (t80) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.3213 time to fit residues: 27.6246 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.120755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.111963 restraints weight = 32799.989| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 4.79 r_work: 0.3848 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 3338 Z= 0.128 Angle : 0.620 5.894 4540 Z= 0.321 Chirality : 0.045 0.226 485 Planarity : 0.006 0.100 592 Dihedral : 7.688 75.527 468 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.88 % Favored : 94.63 % Rotamer: Outliers : 1.98 % Allowed : 15.54 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.29 (0.40), residues: 410 helix: -2.57 (0.78), residues: 28 sheet: -0.51 (0.43), residues: 148 loop : -0.80 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.011 0.001 PHE A 67 TYR 0.009 0.001 TYR C 505 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 115) hydrogen bonds : angle 6.31196 ( 279) SS BOND : bond 0.00412 ( 4) SS BOND : angle 1.21405 ( 8) covalent geometry : bond 0.00318 ( 3334) covalent geometry : angle 0.61856 ( 4532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8230 (ptt90) REVERT: C 347 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.7704 (t80) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.3058 time to fit residues: 26.9941 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN C 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.120789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.111761 restraints weight = 33809.886| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 4.85 r_work: 0.3853 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3338 Z= 0.140 Angle : 0.590 6.367 4540 Z= 0.306 Chirality : 0.044 0.223 485 Planarity : 0.006 0.092 592 Dihedral : 7.448 74.643 468 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.39 % Favored : 95.12 % Rotamer: Outliers : 2.54 % Allowed : 16.38 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.40), residues: 410 helix: -2.31 (0.82), residues: 28 sheet: -0.53 (0.42), residues: 148 loop : -0.72 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.002 0.001 HIS C 519 PHE 0.018 0.001 PHE A 67 TYR 0.013 0.001 TYR C 369 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 115) hydrogen bonds : angle 6.14587 ( 279) SS BOND : bond 0.00456 ( 4) SS BOND : angle 1.30089 ( 8) covalent geometry : bond 0.00341 ( 3334) covalent geometry : angle 0.58828 ( 4532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 63 average time/residue: 0.3893 time to fit residues: 30.4736 Evaluate side-chains 60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.120460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.111551 restraints weight = 33293.218| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 4.81 r_work: 0.3850 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3338 Z= 0.134 Angle : 0.573 6.093 4540 Z= 0.299 Chirality : 0.045 0.217 485 Planarity : 0.006 0.087 592 Dihedral : 7.257 74.283 468 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.39 % Favored : 95.12 % Rotamer: Outliers : 3.11 % Allowed : 15.54 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.18 (0.41), residues: 410 helix: -2.05 (0.85), residues: 28 sheet: -0.55 (0.41), residues: 154 loop : -0.70 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 94 HIS 0.002 0.001 HIS C 519 PHE 0.006 0.001 PHE C 486 TYR 0.013 0.001 TYR C 369 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 115) hydrogen bonds : angle 5.98944 ( 279) SS BOND : bond 0.00428 ( 4) SS BOND : angle 1.22015 ( 8) covalent geometry : bond 0.00327 ( 3334) covalent geometry : angle 0.57143 ( 4532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8263 (ptt90) REVERT: C 519 HIS cc_start: 0.6453 (OUTLIER) cc_final: 0.6088 (m90) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.3188 time to fit residues: 25.4235 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.121223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.112271 restraints weight = 33215.663| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 4.90 r_work: 0.3858 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3338 Z= 0.110 Angle : 0.553 5.810 4540 Z= 0.286 Chirality : 0.044 0.205 485 Planarity : 0.005 0.083 592 Dihedral : 7.004 73.084 468 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.63 % Favored : 94.88 % Rotamer: Outliers : 3.11 % Allowed : 15.54 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.41), residues: 410 helix: -1.76 (0.89), residues: 28 sheet: -0.47 (0.41), residues: 154 loop : -0.60 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.006 0.001 PHE C 486 TYR 0.014 0.001 TYR C 369 ARG 0.010 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02693 ( 115) hydrogen bonds : angle 5.85941 ( 279) SS BOND : bond 0.00392 ( 4) SS BOND : angle 1.08469 ( 8) covalent geometry : bond 0.00277 ( 3334) covalent geometry : angle 0.55129 ( 4532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8075 (ptt90) REVERT: A 46 GLU cc_start: 0.8253 (tt0) cc_final: 0.7915 (tt0) REVERT: B 96 ARG cc_start: 0.8249 (ttm170) cc_final: 0.8027 (ttp-170) REVERT: C 465 GLU cc_start: 0.8723 (tp30) cc_final: 0.8332 (tt0) REVERT: C 519 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.5994 (m90) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.3128 time to fit residues: 26.3936 Evaluate side-chains 63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.121073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.112137 restraints weight = 32421.425| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 4.86 r_work: 0.3859 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3338 Z= 0.110 Angle : 0.536 5.667 4540 Z= 0.277 Chirality : 0.044 0.201 485 Planarity : 0.005 0.078 592 Dihedral : 6.767 72.903 466 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.63 % Favored : 94.88 % Rotamer: Outliers : 3.11 % Allowed : 16.38 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.95 (0.41), residues: 410 helix: -1.58 (0.89), residues: 28 sheet: -0.42 (0.43), residues: 144 loop : -0.57 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.006 0.001 PHE C 486 TYR 0.014 0.001 TYR C 369 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02702 ( 115) hydrogen bonds : angle 5.81461 ( 279) SS BOND : bond 0.00384 ( 4) SS BOND : angle 1.03593 ( 8) covalent geometry : bond 0.00274 ( 3334) covalent geometry : angle 0.53510 ( 4532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8142 (ptt90) REVERT: A 46 GLU cc_start: 0.8322 (tt0) cc_final: 0.7991 (tt0) REVERT: B 96 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7989 (ttp-170) REVERT: C 519 HIS cc_start: 0.6374 (OUTLIER) cc_final: 0.6011 (m90) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.3204 time to fit residues: 25.9416 Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.120344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.111415 restraints weight = 32668.575| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 4.87 r_work: 0.3846 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3338 Z= 0.130 Angle : 0.540 5.739 4540 Z= 0.280 Chirality : 0.044 0.203 485 Planarity : 0.005 0.074 592 Dihedral : 6.680 71.761 466 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.12 % Favored : 94.39 % Rotamer: Outliers : 2.82 % Allowed : 17.23 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.86 (0.41), residues: 410 helix: -1.43 (0.92), residues: 28 sheet: -0.41 (0.43), residues: 144 loop : -0.48 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.003 0.001 HIS C 519 PHE 0.007 0.001 PHE C 486 TYR 0.014 0.001 TYR C 369 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 115) hydrogen bonds : angle 5.70698 ( 279) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.06481 ( 8) covalent geometry : bond 0.00313 ( 3334) covalent geometry : angle 0.53887 ( 4532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8132 (ptt90) REVERT: A 46 GLU cc_start: 0.8384 (tt0) cc_final: 0.8097 (tt0) REVERT: C 465 GLU cc_start: 0.8780 (tp30) cc_final: 0.8389 (tt0) REVERT: C 519 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.6074 (m90) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.3485 time to fit residues: 25.9176 Evaluate side-chains 62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.120886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.112274 restraints weight = 32991.833| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 4.73 r_work: 0.3869 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3338 Z= 0.101 Angle : 0.526 4.557 4540 Z= 0.271 Chirality : 0.043 0.133 485 Planarity : 0.005 0.050 592 Dihedral : 6.161 71.065 464 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.12 % Rotamer: Outliers : 2.54 % Allowed : 16.95 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.87 (0.41), residues: 410 helix: -1.58 (0.88), residues: 28 sheet: -0.39 (0.43), residues: 144 loop : -0.49 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 436 HIS 0.002 0.001 HIS C 519 PHE 0.016 0.001 PHE C 347 TYR 0.014 0.001 TYR C 369 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02609 ( 115) hydrogen bonds : angle 5.66428 ( 279) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.88557 ( 8) covalent geometry : bond 0.00244 ( 3334) covalent geometry : angle 0.52553 ( 4532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8095 (ptt90) REVERT: A 46 GLU cc_start: 0.8342 (tt0) cc_final: 0.8060 (tt0) REVERT: C 465 GLU cc_start: 0.8731 (tp30) cc_final: 0.8360 (tt0) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.4396 time to fit residues: 34.6960 Evaluate side-chains 64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.120949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.112159 restraints weight = 33107.157| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 4.87 r_work: 0.3863 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3338 Z= 0.102 Angle : 0.524 4.878 4540 Z= 0.269 Chirality : 0.043 0.133 485 Planarity : 0.005 0.060 592 Dihedral : 6.163 71.430 464 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.61 % Favored : 94.15 % Rotamer: Outliers : 1.98 % Allowed : 17.80 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.78 (0.41), residues: 410 helix: -1.82 (0.84), residues: 28 sheet: -0.15 (0.44), residues: 134 loop : -0.51 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS C 519 PHE 0.013 0.001 PHE C 347 TYR 0.015 0.001 TYR C 369 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.02589 ( 115) hydrogen bonds : angle 5.57294 ( 279) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.91021 ( 8) covalent geometry : bond 0.00250 ( 3334) covalent geometry : angle 0.52284 ( 4532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 465 GLU cc_start: 0.8746 (tp30) cc_final: 0.8378 (tt0) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.3416 time to fit residues: 26.4674 Evaluate side-chains 61 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 472 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.119751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.111039 restraints weight = 33314.051| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 4.76 r_work: 0.3845 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3338 Z= 0.144 Angle : 0.551 5.456 4540 Z= 0.285 Chirality : 0.043 0.134 485 Planarity : 0.005 0.054 592 Dihedral : 6.120 72.291 464 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.85 % Favored : 93.90 % Rotamer: Outliers : 1.69 % Allowed : 18.08 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.86 (0.42), residues: 410 helix: -1.89 (0.86), residues: 28 sheet: -0.39 (0.42), residues: 144 loop : -0.42 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS C 519 PHE 0.014 0.001 PHE C 347 TYR 0.014 0.001 TYR C 369 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02699 ( 115) hydrogen bonds : angle 5.60848 ( 279) SS BOND : bond 0.00405 ( 4) SS BOND : angle 1.09368 ( 8) covalent geometry : bond 0.00336 ( 3334) covalent geometry : angle 0.54917 ( 4532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7153.42 seconds wall clock time: 128 minutes 6.93 seconds (7686.93 seconds total)