Starting phenix.real_space_refine on Wed Mar 5 16:28:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0x_26952/03_2025/7v0x_26952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0x_26952/03_2025/7v0x_26952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v0x_26952/03_2025/7v0x_26952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0x_26952/03_2025/7v0x_26952.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0x_26952/03_2025/7v0x_26952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0x_26952/03_2025/7v0x_26952.cif" } resolution = 3.0 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= 0.264 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 9 5.16 5 C 1769 2.51 5 N 519 2.21 5 O 521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2818 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 2818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 2807 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 375, 2807 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 2849 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG J 591 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG J 591 " occ=0.55 Time building chain proxies: 3.85, per 1000 atoms: 1.37 Number of scatterers: 2818 At special positions: 0 Unit cell: (95.45, 85.905, 61.835, 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 9 16.00 O 521 8.00 N 519 7.00 C 1769 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=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 652.2 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 61.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'J' and resid 439 through 448 Processing helix chain 'J' and resid 449 through 460 Processing helix chain 'J' and resid 472 through 481 Processing helix chain 'J' and resid 482 through 493 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 515 through 525 Processing helix chain 'J' and resid 538 through 547 Processing helix chain 'J' and resid 548 through 558 Processing helix chain 'J' and resid 571 through 579 Processing helix chain 'J' and resid 581 through 592 Proline residue: J 590 - end of helix Processing helix chain 'J' and resid 604 through 612 Processing helix chain 'J' and resid 614 through 624 Processing helix chain 'J' and resid 637 through 645 Processing helix chain 'J' and resid 647 through 656 Processing helix chain 'J' and resid 670 through 679 Processing helix chain 'J' and resid 680 through 691 Processing helix chain 'J' and resid 703 through 712 Processing helix chain 'J' and resid 713 through 723 Processing helix chain 'J' and resid 736 through 745 Processing helix chain 'J' and resid 746 through 756 Processing helix chain 'J' and resid 769 through 777 Processing helix chain 'J' and resid 779 through 790 removed outlier: 3.897A pdb=" N VAL J 788 " --> pdb=" O ASP J 784 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL J 789 " --> pdb=" O VAL J 785 " (cutoff:3.500A) 137 hydrogen bonds defined for protein. 411 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: 0.84 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 963 1.34 - 1.46: 496 1.46 - 1.58: 1398 1.58 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2873 Sorted by residual: bond pdb=" CA LYS J 460 " pdb=" CB LYS J 460 " ideal model delta sigma weight residual 1.521 1.538 -0.018 1.48e-02 4.57e+03 1.43e+00 bond pdb=" C VAL J 681 " pdb=" N PRO J 682 " ideal model delta sigma weight residual 1.335 1.345 -0.011 1.28e-02 6.10e+03 7.04e-01 bond pdb=" CA LEU J 589 " pdb=" C LEU J 589 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 6.91e-01 bond pdb=" CA VAL J 681 " pdb=" CB VAL J 681 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.36e-01 bond pdb=" C LEU J 589 " pdb=" N PRO J 590 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.33e-01 ... (remaining 2868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 3767 1.44 - 2.88: 112 2.88 - 4.32: 25 4.32 - 5.76: 4 5.76 - 7.20: 2 Bond angle restraints: 3910 Sorted by residual: angle pdb=" C LYS J 468 " pdb=" N ASP J 469 " pdb=" CA ASP J 469 " ideal model delta sigma weight residual 123.05 126.53 -3.48 1.57e+00 4.06e-01 4.91e+00 angle pdb=" C LYS J 525 " pdb=" N GLU J 526 " pdb=" CA GLU J 526 " ideal model delta sigma weight residual 122.35 125.42 -3.07 1.46e+00 4.69e-01 4.43e+00 angle pdb=" C GLN J 458 " pdb=" N ASN J 459 " pdb=" CA ASN J 459 " ideal model delta sigma weight residual 120.89 117.77 3.12 1.50e+00 4.44e-01 4.32e+00 angle pdb=" CA LEU J 777 " pdb=" CB LEU J 777 " pdb=" CG LEU J 777 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" C HIS J 723 " pdb=" N GLN J 724 " pdb=" CA GLN J 724 " ideal model delta sigma weight residual 122.35 125.33 -2.98 1.46e+00 4.69e-01 4.17e+00 ... (remaining 3905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1459 17.15 - 34.31: 177 34.31 - 51.46: 81 51.46 - 68.61: 20 68.61 - 85.76: 4 Dihedral angle restraints: 1741 sinusoidal: 660 harmonic: 1081 Sorted by residual: dihedral pdb=" CA ARG J 558 " pdb=" C ARG J 558 " pdb=" N ASP J 559 " pdb=" CA ASP J 559 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP J 470 " pdb=" CB ASP J 470 " pdb=" CG ASP J 470 " pdb=" OD1 ASP J 470 " ideal model delta sinusoidal sigma weight residual -30.00 -83.79 53.79 1 2.00e+01 2.50e-03 9.82e+00 dihedral pdb=" CA LEU J 587 " pdb=" CB LEU J 587 " pdb=" CG LEU J 587 " pdb=" CD1 LEU J 587 " ideal model delta sinusoidal sigma weight residual 60.00 118.08 -58.08 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 306 0.027 - 0.055: 81 0.055 - 0.082: 47 0.082 - 0.109: 29 0.109 - 0.137: 2 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA ILE J 813 " pdb=" N ILE J 813 " pdb=" C ILE J 813 " pdb=" CB ILE J 813 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA LEU J 777 " pdb=" N LEU J 777 " pdb=" C LEU J 777 " pdb=" CB LEU J 777 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA GLU J 526 " pdb=" N GLU J 526 " pdb=" C GLU J 526 " pdb=" CB GLU J 526 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.95e-01 ... (remaining 462 not shown) Planarity restraints: 507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 439 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO J 440 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 440 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 440 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 670 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO J 671 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 671 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 671 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 637 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO J 638 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 638 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 638 " 0.021 5.00e-02 4.00e+02 ... (remaining 504 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 310 2.75 - 3.29: 2680 3.29 - 3.82: 5094 3.82 - 4.36: 5974 4.36 - 4.90: 9758 Nonbonded interactions: 23816 Sorted by model distance: nonbonded pdb=" O LEU J 786 " pdb=" OG1 THR J 790 " model vdw 2.211 3.040 nonbonded pdb=" N ASN J 484 " pdb=" OD1 ASN J 484 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN J 529 " pdb=" O ARG J 558 " model vdw 2.325 3.120 nonbonded pdb=" O ALA J 676 " pdb=" ND2 ASN J 713 " model vdw 2.392 3.120 nonbonded pdb=" OG1 THR J 439 " pdb=" ND1 HIS J 442 " model vdw 2.423 3.120 ... (remaining 23811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.670 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:15.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.002 0.027 2873 Z= 0.152 Angle : 0.628 7.197 3910 Z= 0.347 Chirality : 0.038 0.137 465 Planarity : 0.005 0.040 507 Dihedral : 19.061 85.765 1043 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.05 % Allowed : 24.58 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.41), residues: 374 helix: 0.63 (0.32), residues: 234 sheet: None (None), residues: 0 loop : 0.48 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 600 HIS 0.004 0.001 HIS J 515 PHE 0.006 0.001 PHE J 719 TYR 0.013 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.335 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.9861 time to fit residues: 70.1703 Evaluate side-chains 65 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 459 ASN Chi-restraints excluded: chain J residue 460 LYS Chi-restraints excluded: chain J residue 472 THR Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain J residue 509 ILE Chi-restraints excluded: chain J residue 667 SER Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 730 LYS Chi-restraints excluded: chain J residue 736 SER Chi-restraints excluded: chain J residue 747 THR Chi-restraints excluded: chain J residue 788 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 578 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.138716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.109138 restraints weight = 11472.250| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.06 r_work: 0.2839 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2873 Z= 0.168 Angle : 0.524 5.149 3910 Z= 0.264 Chirality : 0.039 0.141 465 Planarity : 0.005 0.032 507 Dihedral : 8.770 50.839 418 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.71 % Allowed : 25.59 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.42), residues: 374 helix: 1.13 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.77 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 449 PHE 0.006 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.319 Fit side-chains REVERT: J 484 ASN cc_start: 0.6487 (OUTLIER) cc_final: 0.6170 (p0) REVERT: J 692 VAL cc_start: 0.8553 (t) cc_final: 0.8309 (m) REVERT: J 700 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7444 (mtm) outliers start: 13 outliers final: 5 residues processed: 64 average time/residue: 0.9241 time to fit residues: 61.1474 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 730 LYS Chi-restraints excluded: chain J residue 747 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 0.0060 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 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 = 0.3430 r_free = 0.3430 target = 0.139419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.108666 restraints weight = 10649.399| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.05 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2873 Z= 0.143 Angle : 0.501 5.394 3910 Z= 0.249 Chirality : 0.038 0.129 465 Planarity : 0.004 0.031 507 Dihedral : 6.578 51.392 405 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.38 % Allowed : 24.58 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.43), residues: 374 helix: 1.42 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.84 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.005 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.003 0.000 ARG J 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.302 Fit side-chains REVERT: J 550 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6980 (mmt90) REVERT: J 692 VAL cc_start: 0.8352 (t) cc_final: 0.8152 (m) outliers start: 12 outliers final: 5 residues processed: 59 average time/residue: 1.0772 time to fit residues: 65.4805 Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 716 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 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 = 0.3442 r_free = 0.3442 target = 0.140281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.111413 restraints weight = 9556.091| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.86 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2873 Z= 0.144 Angle : 0.492 5.277 3910 Z= 0.245 Chirality : 0.038 0.129 465 Planarity : 0.004 0.032 507 Dihedral : 5.415 39.943 398 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.03 % Allowed : 25.93 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.43), residues: 374 helix: 1.54 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.84 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.005 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.292 Fit side-chains REVERT: J 550 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7039 (mmt90) REVERT: J 692 VAL cc_start: 0.8320 (t) cc_final: 0.8088 (m) REVERT: J 700 MET cc_start: 0.7731 (mtm) cc_final: 0.6688 (mtp) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 1.0038 time to fit residues: 60.1172 Evaluate side-chains 60 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 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 = 0.3371 r_free = 0.3371 target = 0.134256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.105033 restraints weight = 6690.870| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.31 r_work: 0.2803 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2873 Z= 0.282 Angle : 0.560 5.850 3910 Z= 0.283 Chirality : 0.042 0.138 465 Planarity : 0.005 0.035 507 Dihedral : 5.828 47.312 398 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.38 % Allowed : 25.25 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.43), residues: 374 helix: 1.28 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.79 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 600 HIS 0.005 0.002 HIS J 739 PHE 0.005 0.002 PHE J 719 TYR 0.011 0.002 TYR J 735 ARG 0.002 0.000 ARG J 512 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.328 Fit side-chains REVERT: J 550 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7562 (mmt90) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 1.0350 time to fit residues: 60.8230 Evaluate side-chains 56 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 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 = 0.3426 r_free = 0.3426 target = 0.139077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.109300 restraints weight = 8419.065| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.57 r_work: 0.2841 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2873 Z= 0.132 Angle : 0.486 5.135 3910 Z= 0.242 Chirality : 0.038 0.127 465 Planarity : 0.005 0.032 507 Dihedral : 5.721 55.002 398 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.37 % Allowed : 25.93 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.43), residues: 374 helix: 1.53 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.91 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.297 Fit side-chains REVERT: J 550 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7587 (mmt90) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.9975 time to fit residues: 55.5930 Evaluate side-chains 58 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 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 = 0.3373 r_free = 0.3373 target = 0.134360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.103842 restraints weight = 8069.331| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.58 r_work: 0.2783 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2873 Z= 0.260 Angle : 0.543 5.984 3910 Z= 0.275 Chirality : 0.041 0.138 465 Planarity : 0.005 0.035 507 Dihedral : 5.573 55.207 396 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.05 % Allowed : 24.24 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.43), residues: 374 helix: 1.30 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.83 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 600 HIS 0.005 0.002 HIS J 723 PHE 0.005 0.002 PHE J 537 TYR 0.012 0.002 TYR J 735 ARG 0.001 0.000 ARG J 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.305 Fit side-chains REVERT: J 550 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7554 (mmt90) REVERT: J 700 MET cc_start: 0.8735 (mtm) cc_final: 0.7511 (mtp) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 1.1437 time to fit residues: 63.5439 Evaluate side-chains 57 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Chi-restraints excluded: chain J residue 768 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 492 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 = 0.3408 r_free = 0.3408 target = 0.137123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.105936 restraints weight = 10489.952| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.87 r_work: 0.2800 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2873 Z= 0.146 Angle : 0.488 5.502 3910 Z= 0.245 Chirality : 0.038 0.129 465 Planarity : 0.005 0.033 507 Dihedral : 5.519 58.340 396 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.03 % Allowed : 25.93 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.86 (0.44), residues: 374 helix: 1.53 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.94 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.328 Fit side-chains REVERT: J 550 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7623 (mmt90) REVERT: J 700 MET cc_start: 0.8669 (mtm) cc_final: 0.7436 (mtp) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.9723 time to fit residues: 53.2750 Evaluate side-chains 54 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 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 = 0.3405 r_free = 0.3405 target = 0.136912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.107347 restraints weight = 7153.072| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.40 r_work: 0.2835 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2873 Z= 0.172 Angle : 0.505 6.407 3910 Z= 0.251 Chirality : 0.039 0.131 465 Planarity : 0.005 0.034 507 Dihedral : 4.327 18.220 394 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.04 % Allowed : 25.25 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.43), residues: 374 helix: 1.51 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.91 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.330 Fit side-chains REVERT: J 550 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7598 (mmt90) REVERT: J 700 MET cc_start: 0.8623 (mtm) cc_final: 0.7400 (mtp) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 1.0046 time to fit residues: 54.9894 Evaluate side-chains 56 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 0.0670 chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.9578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 HIS ** 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 = 0.3411 r_free = 0.3411 target = 0.137838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.108477 restraints weight = 7645.398| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.43 r_work: 0.2859 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2873 Z= 0.153 Angle : 0.491 5.757 3910 Z= 0.245 Chirality : 0.038 0.129 465 Planarity : 0.005 0.034 507 Dihedral : 4.276 17.659 394 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.69 % Allowed : 26.60 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.43), residues: 374 helix: 1.57 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.94 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.298 Fit side-chains REVERT: J 550 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7570 (mmt90) REVERT: J 700 MET cc_start: 0.8595 (mtm) cc_final: 0.7362 (mtp) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 1.0687 time to fit residues: 56.2169 Evaluate side-chains 52 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 501 THR Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 736 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 HIS ** 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 = 0.3421 r_free = 0.3421 target = 0.138368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.107879 restraints weight = 9437.148| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.72 r_work: 0.2825 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2873 Z= 0.148 Angle : 0.486 5.612 3910 Z= 0.242 Chirality : 0.038 0.128 465 Planarity : 0.005 0.034 507 Dihedral : 4.219 17.984 394 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.36 % Allowed : 26.94 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.93 (0.43), residues: 374 helix: 1.60 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.92 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.004 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3027.30 seconds wall clock time: 52 minutes 31.55 seconds (3151.55 seconds total)