Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:59:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/11_2022/7v0x_26952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/11_2022/7v0x_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_26952/11_2022/7v0x_26952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/11_2022/7v0x_26952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/11_2022/7v0x_26952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/11_2022/7v0x_26952.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "J ASP 470": "OD1" <-> "OD2" Residue "J GLU 524": "OE1" <-> "OE2" Residue "J GLU 526": "OE1" <-> "OE2" Residue "J ASP 559": "OD1" <-> "OD2" Residue "J PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 808": "OE1" <-> "OE2" Residue "J ASP 811": "OD1" <-> "OD2" Residue "J GLU 812": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.96, per 1000 atoms: 1.05 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 - 3.50 Amino acid : False - 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: 0.91 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.11 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: 0.82 Time building geometry restraints manager: 1.00 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: 99.87 - 106.68: 107 106.68 - 113.48: 1681 113.48 - 120.29: 912 120.29 - 127.09: 1164 127.09 - 133.90: 46 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 2.440 nonbonded pdb=" N ASN J 484 " pdb=" OD1 ASN J 484 " model vdw 2.299 2.520 nonbonded pdb=" NE2 GLN J 529 " pdb=" O ARG J 558 " model vdw 2.325 2.520 nonbonded pdb=" O ALA J 676 " pdb=" ND2 ASN J 713 " model vdw 2.392 2.520 nonbonded pdb=" OG1 THR J 439 " pdb=" ND1 HIS J 442 " model vdw 2.423 2.520 ... (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 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. 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: 0.680 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: 0.000 Extract box with map and model: 3.660 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 13.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 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 : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 5.05 % 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 *********************** 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 : 0.280 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.9584 time to fit residues: 68.3165 Evaluate side-chains 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.4980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 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 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 2873 Z= 0.154 Angle : 0.513 5.329 3910 Z= 0.258 Chirality : 0.038 0.141 465 Planarity : 0.005 0.032 507 Dihedral : 4.508 18.421 394 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 7.07 % 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: 1.42 (0.42), residues: 374 helix: 1.17 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.77 (0.51), residues: 139 *********************** 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 74 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 0.350 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 69 average time/residue: 0.8197 time to fit residues: 58.7383 Evaluate side-chains 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.0299 time to fit residues: 0.5148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2873 Z= 0.198 Angle : 0.530 6.373 3910 Z= 0.265 Chirality : 0.039 0.135 465 Planarity : 0.004 0.031 507 Dihedral : 4.499 18.656 394 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 6.73 % 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: 1.43 (0.42), residues: 374 helix: 1.24 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.65 (0.52), residues: 139 *********************** 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 71 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 0.341 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 67 average time/residue: 0.8716 time to fit residues: 60.4789 Evaluate side-chains 67 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.328 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.9104 time to fit residues: 2.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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: 0.8800 moved from start: 0.1175 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= 0.119 Angle : 0.485 5.646 3910 Z= 0.239 Chirality : 0.037 0.129 465 Planarity : 0.004 0.030 507 Dihedral : 4.247 17.621 394 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 5.39 % 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: 1.60 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.71 (0.52), residues: 139 *********************** 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 70 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.344 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 69 average time/residue: 0.8429 time to fit residues: 60.2579 Evaluate side-chains 68 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.5390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- 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 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2873 Z= 0.193 Angle : 0.515 6.264 3910 Z= 0.257 Chirality : 0.039 0.135 465 Planarity : 0.004 0.032 507 Dihedral : 4.376 18.459 394 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 6.06 % 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: 1.60 (0.43), residues: 374 helix: 1.43 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.62 (0.53), residues: 139 *********************** 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 69 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.361 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.8574 time to fit residues: 58.5865 Evaluate side-chains 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.6244 time to fit residues: 2.1256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8837 moved from start: 0.1301 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= 0.160 Angle : 0.506 6.008 3910 Z= 0.251 Chirality : 0.038 0.133 465 Planarity : 0.004 0.031 507 Dihedral : 4.330 17.844 394 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 5.72 % 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: 1.69 (0.43), residues: 374 helix: 1.50 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.66 (0.53), residues: 139 *********************** 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 67 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.343 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 65 average time/residue: 0.8982 time to fit residues: 60.3850 Evaluate side-chains 64 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.0297 time to fit residues: 0.5260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1302 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= 0.139 Angle : 0.490 5.731 3910 Z= 0.243 Chirality : 0.037 0.131 465 Planarity : 0.004 0.031 507 Dihedral : 4.252 18.039 394 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 5.05 % 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: 1.80 (0.43), residues: 374 helix: 1.58 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.70 (0.54), residues: 139 *********************** 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 66 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.343 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.8705 time to fit residues: 58.6067 Evaluate side-chains 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.0010 overall best weight: 1.5992 ------------------------------------------------------------------------------- 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 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2873 Z= 0.184 Angle : 0.511 6.087 3910 Z= 0.254 Chirality : 0.039 0.135 465 Planarity : 0.004 0.032 507 Dihedral : 4.355 18.257 394 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 6.06 % 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: 1.66 (0.43), residues: 374 helix: 1.45 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.70 (0.54), residues: 139 *********************** 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 68 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.361 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 66 average time/residue: 0.8850 time to fit residues: 60.4428 Evaluate side-chains 66 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.7802 time to fit residues: 2.0623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.8814 moved from start: 0.1362 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= 0.126 Angle : 0.484 5.624 3910 Z= 0.239 Chirality : 0.037 0.130 465 Planarity : 0.004 0.031 507 Dihedral : 4.210 17.716 394 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 5.39 % 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: 1.64 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.69 (0.54), residues: 139 *********************** 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 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.335 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.8429 time to fit residues: 56.8173 Evaluate side-chains 62 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.4702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.0570 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.8798 moved from start: 0.1391 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= 0.121 Angle : 0.491 5.723 3910 Z= 0.242 Chirality : 0.037 0.128 465 Planarity : 0.004 0.031 507 Dihedral : 4.103 17.631 394 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 4.71 % 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: 1.92 (0.43), residues: 374 helix: 1.72 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.68 (0.54), residues: 139 ********************** 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 62 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.339 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 62 average time/residue: 0.8105 time to fit residues: 52.1775 Evaluate side-chains 61 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.4220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.137119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.106930 restraints weight = 9661.683| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.92 r_work: 0.2966 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work: 0.2882 rms_B_bonded: 3.26 restraints_weight: 0.1250 r_work: 0.2817 rms_B_bonded: 4.17 restraints_weight: 0.0625 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1402 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= 0.167 Angle : 0.510 5.996 3910 Z= 0.253 Chirality : 0.038 0.132 465 Planarity : 0.004 0.032 507 Dihedral : 4.265 17.938 394 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 5.05 % 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: 1.56 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.60 (0.54), residues: 139 =============================================================================== Job complete usr+sys time: 1817.14 seconds wall clock time: 33 minutes 6.93 seconds (1986.93 seconds total)