Starting phenix.real_space_refine on Sun Mar 10 15:17:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/03_2024/7v0x_26952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/03_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_26952/03_2024/7v0x_26952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/03_2024/7v0x_26952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/03_2024/7v0x_26952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0x_26952/03_2024/7v0x_26952.pdb" } 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 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-5265/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: 3.50, per 1000 atoms: 1.24 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: 1.23 Conformation dependent library (CDL) restraints added in 1.1 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: 0.28 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: 0.73 Time building geometry restraints manager: 1.29 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 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: 0.780 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: 3.920 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.690 Find NCS groups from input model: 0.090 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- 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 : 0.335 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 1.0383 time to fit residues: 73.8721 Evaluate side-chains 65 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8550 moved from start: 0.0871 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= 0.133 Angle : 0.503 5.025 3910 Z= 0.251 Chirality : 0.037 0.136 465 Planarity : 0.005 0.033 507 Dihedral : 8.440 56.232 418 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 1.49 (0.42), residues: 374 helix: 1.23 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.82 (0.51), 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 607 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 : 0.329 Fit side-chains REVERT: J 557 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7042 (tp30) REVERT: J 700 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7385 (mtm) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 0.8536 time to fit residues: 55.7943 Evaluate side-chains 58 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 472 THR 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 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: 3.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1088 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= 0.117 Angle : 0.485 5.259 3910 Z= 0.239 Chirality : 0.037 0.126 465 Planarity : 0.004 0.029 507 Dihedral : 6.066 52.882 402 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.03 % Allowed : 25.93 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.42), residues: 374 helix: 1.58 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.71 (0.51), 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 0.001 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: 8 poor density : 54 time to evaluate : 0.328 Fit side-chains REVERT: J 550 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7229 (mmt90) REVERT: J 700 MET cc_start: 0.7828 (mtp) cc_final: 0.7399 (mtm) REVERT: J 768 THR cc_start: 0.7854 (p) cc_final: 0.7509 (t) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.9543 time to fit residues: 58.1633 Evaluate side-chains 61 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 526 GLU Chi-restraints excluded: chain J residue 550 ARG Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 716 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8560 moved from start: 0.1198 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= 0.131 Angle : 0.488 5.183 3910 Z= 0.242 Chirality : 0.037 0.131 465 Planarity : 0.004 0.031 507 Dihedral : 5.984 51.333 400 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.70 % Allowed : 26.94 % Favored : 69.36 % 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: 1.84 (0.43), residues: 374 helix: 1.61 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.73 (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 607 PHE 0.006 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.307 Fit side-chains REVERT: J 550 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7265 (mmt90) REVERT: J 700 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7427 (mtm) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.9478 time to fit residues: 56.7853 Evaluate side-chains 63 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- 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: 0.8584 moved from start: 0.1257 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= 0.166 Angle : 0.498 5.076 3910 Z= 0.248 Chirality : 0.038 0.131 465 Planarity : 0.004 0.031 507 Dihedral : 6.127 50.554 400 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.38 % Allowed : 26.26 % Favored : 69.36 % 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: 1.59 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.71 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.005 0.001 HIS J 607 PHE 0.005 0.001 PHE J 719 TYR 0.008 0.001 TYR J 624 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 66 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.336 Fit side-chains REVERT: J 471 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: J 550 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7171 (mmt90) REVERT: J 700 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7438 (mtm) outliers start: 12 outliers final: 7 residues processed: 59 average time/residue: 1.0151 time to fit residues: 61.7948 Evaluate side-chains 61 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 471 GLN 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 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 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: 0.2980 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8569 moved from start: 0.1297 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 : 0.481 5.169 3910 Z= 0.239 Chirality : 0.037 0.130 465 Planarity : 0.004 0.031 507 Dihedral : 6.200 55.834 400 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.04 % Allowed : 26.94 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.43), residues: 374 helix: 1.68 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.71 (0.53), 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 607 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 *********************** 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 62 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.333 Fit side-chains REVERT: J 471 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7383 (mt0) REVERT: J 550 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7275 (mmt90) REVERT: J 700 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7437 (mtm) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 1.0158 time to fit residues: 57.7128 Evaluate side-chains 61 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 471 GLN 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 587 LEU Chi-restraints excluded: chain J residue 700 MET Chi-restraints excluded: chain J residue 716 LEU 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: 0.6980 chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8558 moved from start: 0.1341 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= 0.128 Angle : 0.471 5.433 3910 Z= 0.234 Chirality : 0.037 0.128 465 Planarity : 0.004 0.031 507 Dihedral : 5.872 55.770 398 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.37 % Allowed : 27.27 % Favored : 69.36 % 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 (0.43), residues: 374 helix: 1.74 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.67 (0.53), 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 607 PHE 0.004 0.001 PHE J 719 TYR 0.008 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 58 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.291 Fit side-chains REVERT: J 471 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: J 550 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7275 (mmt90) REVERT: J 700 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7449 (mtm) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.9819 time to fit residues: 53.7489 Evaluate side-chains 57 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 471 GLN Chi-restraints excluded: chain J residue 484 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.0060 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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: 0.8557 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2873 Z= 0.133 Angle : 0.482 6.804 3910 Z= 0.236 Chirality : 0.037 0.128 465 Planarity : 0.004 0.031 507 Dihedral : 4.762 48.261 396 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.04 % Allowed : 26.60 % Favored : 69.36 % 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 (0.43), residues: 374 helix: 1.74 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.67 (0.53), 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 607 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 546 ARG 0.001 0.000 ARG J 803 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.321 Fit side-chains REVERT: J 471 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7324 (mt0) REVERT: J 550 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7274 (mmt90) REVERT: J 700 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7441 (mtm) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.9377 time to fit residues: 54.3541 Evaluate side-chains 60 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 471 GLN Chi-restraints excluded: chain J residue 484 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.0010 chunk 29 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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: 0.8540 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2873 Z= 0.120 Angle : 0.471 5.644 3910 Z= 0.231 Chirality : 0.036 0.125 465 Planarity : 0.004 0.030 507 Dihedral : 4.648 46.447 396 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.70 % Allowed : 26.94 % Favored : 69.36 % 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: 2.00 (0.43), residues: 374 helix: 1.81 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.65 (0.53), 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 607 PHE 0.004 0.001 PHE J 719 TYR 0.008 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 60 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.289 Fit side-chains REVERT: J 471 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: J 550 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7264 (mmt90) REVERT: J 700 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7455 (mtm) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.9186 time to fit residues: 53.2477 Evaluate side-chains 58 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 471 GLN Chi-restraints excluded: chain J residue 484 ASN 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 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: 0.1980 chunk 22 optimal weight: 0.0870 chunk 17 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.0030 chunk 30 optimal weight: 5.9990 overall best weight: 0.2466 ------------------------------------------------------------------------------- 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 690 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 0.021 2873 Z= 0.105 Angle : 0.461 5.730 3910 Z= 0.226 Chirality : 0.036 0.122 465 Planarity : 0.004 0.030 507 Dihedral : 4.474 43.524 396 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.03 % Allowed : 27.95 % Favored : 69.02 % 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: 2.11 (0.43), residues: 374 helix: 1.94 (0.34), residues: 235 sheet: None (None), residues: 0 loop : 0.61 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 600 HIS 0.005 0.001 HIS J 442 PHE 0.004 0.001 PHE J 719 TYR 0.007 0.001 TYR J 546 ARG 0.002 0.000 ARG J 803 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.337 Fit side-chains REVERT: J 550 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7271 (mmt90) REVERT: J 700 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7441 (mtm) REVERT: J 768 THR cc_start: 0.7824 (p) cc_final: 0.7522 (t) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 1.0524 time to fit residues: 54.4185 Evaluate side-chains 50 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 484 ASN 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: 2.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.138644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.107589 restraints weight = 9839.375| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.80 r_work: 0.2827 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2873 Z= 0.176 Angle : 0.498 6.164 3910 Z= 0.247 Chirality : 0.038 0.130 465 Planarity : 0.004 0.032 507 Dihedral : 4.635 42.454 396 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.69 % Allowed : 27.95 % Favored : 69.36 % 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: 1.78 (0.43), residues: 374 helix: 1.61 (0.33), residues: 235 sheet: None (None), residues: 0 loop : 0.60 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 600 HIS 0.005 0.001 HIS J 607 PHE 0.004 0.001 PHE J 719 TYR 0.008 0.001 TYR J 735 ARG 0.001 0.000 ARG J 803 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.87 seconds wall clock time: 36 minutes 21.31 seconds (2181.31 seconds total)