Starting phenix.real_space_refine on Mon Sep 23 12:54:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/09_2024/7v0x_26952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/09_2024/7v0x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/09_2024/7v0x_26952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/09_2024/7v0x_26952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/09_2024/7v0x_26952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/09_2024/7v0x_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-5461/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: 3.68, per 1000 atoms: 1.31 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: 0.71 Conformation dependent library (CDL) restraints added in 677.9 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: 0.74 Time building geometry restraints manager: 0.81 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: 0.740 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: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.030 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.339 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.9625 time to fit residues: 68.4104 Evaluate side-chains 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.312 Fit side-chains REVERT: J 484 ASN cc_start: 0.6372 (OUTLIER) cc_final: 0.6050 (p0) REVERT: J 692 VAL cc_start: 0.8517 (t) cc_final: 0.8308 (m) REVERT: J 700 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7396 (mtm) outliers start: 13 outliers final: 5 residues processed: 64 average time/residue: 0.9160 time to fit residues: 60.5633 Evaluate side-chains 59 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1129 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= 0.141 Angle : 0.499 5.352 3910 Z= 0.248 Chirality : 0.038 0.128 465 Planarity : 0.004 0.031 507 Dihedral : 6.520 50.767 405 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.70 % Allowed : 24.92 % Favored : 71.38 % 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: 1.71 (0.43), residues: 374 helix: 1.43 (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 62 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.308 Fit side-chains REVERT: J 550 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7148 (mmt90) REVERT: J 692 VAL cc_start: 0.8455 (t) cc_final: 0.8202 (m) REVERT: J 700 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7395 (mtm) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 1.0667 time to fit residues: 62.7522 Evaluate side-chains 58 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 700 MET 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 3 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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 740 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2873 Z= 0.368 Angle : 0.615 6.983 3910 Z= 0.313 Chirality : 0.045 0.147 465 Planarity : 0.005 0.034 507 Dihedral : 6.083 46.340 398 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.39 % Allowed : 24.24 % 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: 1.16 (0.42), residues: 374 helix: 0.99 (0.33), residues: 234 sheet: None (None), residues: 0 loop : 0.63 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 600 HIS 0.007 0.002 HIS J 739 PHE 0.007 0.002 PHE J 537 TYR 0.014 0.002 TYR J 735 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 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.276 Fit side-chains REVERT: J 550 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7229 (mmt90) REVERT: J 700 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7427 (mtm) REVERT: J 803 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6616 (ttm110) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 1.1193 time to fit residues: 65.6422 Evaluate side-chains 61 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 463 VAL 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 700 MET Chi-restraints excluded: chain J residue 716 LEU Chi-restraints excluded: chain J residue 736 SER Chi-restraints excluded: chain J residue 768 THR Chi-restraints excluded: chain J residue 803 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 740 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2873 Z= 0.165 Angle : 0.511 5.247 3910 Z= 0.255 Chirality : 0.039 0.133 465 Planarity : 0.005 0.033 507 Dihedral : 5.859 53.014 398 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.05 % Allowed : 23.23 % Favored : 71.72 % 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: 1.56 (0.43), residues: 374 helix: 1.30 (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 0.001 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 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 64 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.275 Fit side-chains REVERT: J 550 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7266 (mmt90) REVERT: J 557 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7013 (tp30) REVERT: J 700 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7406 (mtm) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 1.0175 time to fit residues: 59.7452 Evaluate side-chains 62 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 516 VAL Chi-restraints excluded: chain J residue 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 557 GLU Chi-restraints excluded: chain J residue 587 LEU 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 736 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2873 Z= 0.150 Angle : 0.494 5.380 3910 Z= 0.247 Chirality : 0.038 0.130 465 Planarity : 0.005 0.032 507 Dihedral : 5.854 58.671 398 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.39 % Allowed : 24.24 % 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: 1.77 (0.43), residues: 374 helix: 1.47 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.88 (0.54), 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 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 63 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.304 Fit side-chains REVERT: J 550 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7266 (mmt90) REVERT: J 700 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7418 (mtm) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 0.9892 time to fit residues: 57.1119 Evaluate side-chains 57 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 700 MET 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 20 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 0.0270 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2873 Z= 0.125 Angle : 0.478 5.366 3910 Z= 0.237 Chirality : 0.037 0.125 465 Planarity : 0.004 0.032 507 Dihedral : 4.532 36.011 396 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 26.94 % 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: 2.02 (0.44), residues: 374 helix: 1.65 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 1.02 (0.55), 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 0.009 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 *********************** 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 60 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.300 Fit side-chains REVERT: J 550 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7266 (mmt90) REVERT: J 700 MET cc_start: 0.7842 (mtp) cc_final: 0.7426 (mtm) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 1.0491 time to fit residues: 60.5121 Evaluate side-chains 57 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 736 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1504 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= 0.204 Angle : 0.519 6.068 3910 Z= 0.260 Chirality : 0.040 0.133 465 Planarity : 0.005 0.034 507 Dihedral : 4.316 18.336 394 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.03 % Allowed : 26.94 % Favored : 70.03 % 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: 1.81 (0.43), residues: 374 helix: 1.47 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.96 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 600 HIS 0.005 0.001 HIS J 723 PHE 0.004 0.001 PHE J 719 TYR 0.010 0.002 TYR J 735 ARG 0.001 0.000 ARG J 512 *********************** 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 fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.336 Fit side-chains REVERT: J 550 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7172 (mmt90) REVERT: J 557 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: J 700 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7452 (mtm) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 1.1716 time to fit residues: 61.4405 Evaluate side-chains 55 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 557 GLU Chi-restraints excluded: chain J residue 700 MET 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 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1519 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= 0.149 Angle : 0.494 5.940 3910 Z= 0.245 Chirality : 0.038 0.129 465 Planarity : 0.005 0.033 507 Dihedral : 4.247 17.609 394 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.03 % Allowed : 26.94 % Favored : 70.03 % 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: 1.94 (0.44), residues: 374 helix: 1.57 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 1.01 (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 57 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.325 Fit side-chains REVERT: J 550 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7268 (mmt90) REVERT: J 700 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7443 (mtm) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 1.1320 time to fit residues: 60.5542 Evaluate side-chains 55 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 700 MET Chi-restraints excluded: chain J residue 716 LEU 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 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2873 Z= 0.132 Angle : 0.481 6.023 3910 Z= 0.239 Chirality : 0.037 0.126 465 Planarity : 0.005 0.033 507 Dihedral : 4.163 17.823 394 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.69 % Allowed : 27.27 % Favored : 70.03 % 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: 2.04 (0.44), residues: 374 helix: 1.67 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 1.01 (0.55), 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 442 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 624 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 53 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.315 Fit side-chains REVERT: J 550 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7267 (mmt90) REVERT: J 700 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7432 (mtm) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 1.0853 time to fit residues: 55.9654 Evaluate side-chains 53 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 700 MET Chi-restraints excluded: chain J residue 716 LEU 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 3 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.135176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.104337 restraints weight = 9692.670| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.76 r_work: 0.2781 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2873 Z= 0.236 Angle : 0.535 6.115 3910 Z= 0.268 Chirality : 0.040 0.135 465 Planarity : 0.005 0.035 507 Dihedral : 4.395 18.316 394 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.03 % Allowed : 26.94 % Favored : 70.03 % 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: 1.73 (0.43), residues: 374 helix: 1.41 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.92 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 600 HIS 0.005 0.001 HIS J 723 PHE 0.005 0.002 PHE J 537 TYR 0.011 0.002 TYR J 735 ARG 0.001 0.000 ARG J 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.93 seconds wall clock time: 35 minutes 4.08 seconds (2104.08 seconds total)