Mon 24 Dec 00:28:18 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vk8-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vk8-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:28:23 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 388 and 0 Target number of residues in the AU: 388 Target solvent content: 0.4456 Checking the provided sequence file Detected sequence length: 106 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 424 Adjusted target solvent content: 0.39 Input MTZ file: 1vk8-2.0-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 47.646 47.650 49.609 73.804 62.898 73.615 Input sequence file: 1vk8-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.40 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 41.711 2.000 Wilson plot Bfac: 13.84 23674 reflections ( 95.48 % complete ) and 0 restraints for refining 3757 atoms. Observations/parameters ratio is 1.58 ------------------------------------------------------ Starting model: R = 0.2976 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2391 (Rfree = 0.000) for 3757 atoms. Found 117 (128 requested) and removed 70 (64 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.80 2.09 NCS extension: 0 residues added, 3804 seeds are put forward Round 1: 287 peptides, 23 chains. Longest chain 31 peptides. Score 0.815 Round 2: 320 peptides, 16 chains. Longest chain 70 peptides. Score 0.898 Round 3: 336 peptides, 9 chains. Longest chain 72 peptides. Score 0.939 Round 4: 339 peptides, 10 chains. Longest chain 92 peptides. Score 0.937 Round 5: 345 peptides, 10 chains. Longest chain 93 peptides. Score 0.940 Taking the results from Round 5 Chains 10, Residues 335, Estimated correctness of the model 99.6 % 7 chains (306 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 34 A Built loop between residues 46 C and 49 C Built loop between residues 76 D and 79 D 7 chains (346 residues) following loop building 4 chains (317 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3607 restraints for refining 3288 atoms. 891 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2777 (Rfree = 0.000) for 3288 atoms. Found 88 (112 requested) and removed 59 (56 requested) atoms. Cycle 2: After refmac, R = 0.2535 (Rfree = 0.000) for 3296 atoms. Found 80 (111 requested) and removed 56 (56 requested) atoms. Cycle 3: After refmac, R = 0.2253 (Rfree = 0.000) for 3304 atoms. Found 70 (108 requested) and removed 43 (56 requested) atoms. Cycle 4: After refmac, R = 0.2089 (Rfree = 0.000) for 3312 atoms. Found 84 (107 requested) and removed 29 (57 requested) atoms. Cycle 5: After refmac, R = 0.1998 (Rfree = 0.000) for 3364 atoms. Found 57 (108 requested) and removed 33 (57 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.80 2.09 NCS extension: 7 residues added (30 deleted due to clashes), 3400 seeds are put forward Round 1: 357 peptides, 7 chains. Longest chain 90 peptides. Score 0.956 Round 2: 360 peptides, 5 chains. Longest chain 92 peptides. Score 0.963 Round 3: 359 peptides, 7 chains. Longest chain 90 peptides. Score 0.957 Round 4: 360 peptides, 8 chains. Longest chain 92 peptides. Score 0.954 Round 5: 359 peptides, 7 chains. Longest chain 90 peptides. Score 0.957 Taking the results from Round 2 Chains 5, Residues 355, Estimated correctness of the model 99.8 % 4 chains (345 residues) have been docked in sequence Building loops using Loopy2018 5 chains (355 residues) following loop building 4 chains (345 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3519 restraints for refining 3376 atoms. 665 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2092 (Rfree = 0.000) for 3376 atoms. Found 106 (106 requested) and removed 60 (57 requested) atoms. Cycle 7: After refmac, R = 0.1955 (Rfree = 0.000) for 3419 atoms. Found 80 (105 requested) and removed 52 (58 requested) atoms. Cycle 8: After refmac, R = 0.1868 (Rfree = 0.000) for 3442 atoms. Found 58 (104 requested) and removed 29 (59 requested) atoms. Cycle 9: After refmac, R = 0.1799 (Rfree = 0.000) for 3468 atoms. Found 43 (104 requested) and removed 38 (59 requested) atoms. Cycle 10: After refmac, R = 0.1761 (Rfree = 0.000) for 3471 atoms. Found 60 (101 requested) and removed 21 (59 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.81 2.10 NCS extension: 1 residues added (14 deleted due to clashes), 3511 seeds are put forward Round 1: 360 peptides, 6 chains. Longest chain 92 peptides. Score 0.960 Round 2: 361 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 3: 361 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 4: 363 peptides, 5 chains. Longest chain 93 peptides. Score 0.964 Round 5: 357 peptides, 9 chains. Longest chain 93 peptides. Score 0.949 Taking the results from Round 4 Chains 5, Residues 358, Estimated correctness of the model 99.8 % 5 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 C and 30 C 4 chains (362 residues) following loop building 4 chains (362 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3396 restraints for refining 3423 atoms. 451 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1976 (Rfree = 0.000) for 3423 atoms. Found 97 (101 requested) and removed 63 (58 requested) atoms. Cycle 12: After refmac, R = 0.1853 (Rfree = 0.000) for 3448 atoms. Found 61 (99 requested) and removed 51 (59 requested) atoms. Cycle 13: After refmac, R = 0.1764 (Rfree = 0.000) for 3457 atoms. Found 78 (97 requested) and removed 27 (59 requested) atoms. Cycle 14: After refmac, R = 0.1712 (Rfree = 0.000) for 3506 atoms. Found 50 (98 requested) and removed 35 (60 requested) atoms. Cycle 15: After refmac, R = 0.1682 (Rfree = 0.000) for 3521 atoms. Found 54 (96 requested) and removed 33 (60 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.81 2.10 NCS extension: 1 residues added (28 deleted due to clashes), 3546 seeds are put forward Round 1: 362 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 2: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 3: 361 peptides, 7 chains. Longest chain 91 peptides. Score 0.957 Round 4: 361 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 5: 362 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Taking the results from Round 5 Chains 5, Residues 357, Estimated correctness of the model 99.8 % 5 chains (357 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 29 A 4 chains (360 residues) following loop building 4 chains (360 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3426 restraints for refining 3441 atoms. 503 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1921 (Rfree = 0.000) for 3441 atoms. Found 91 (91 requested) and removed 62 (58 requested) atoms. Cycle 17: After refmac, R = 0.1816 (Rfree = 0.000) for 3464 atoms. Found 75 (90 requested) and removed 58 (59 requested) atoms. Cycle 18: After refmac, R = 0.1742 (Rfree = 0.000) for 3479 atoms. Found 85 (88 requested) and removed 28 (59 requested) atoms. Cycle 19: After refmac, R = 0.1693 (Rfree = 0.000) for 3535 atoms. Found 57 (90 requested) and removed 49 (60 requested) atoms. Cycle 20: After refmac, R = 0.1665 (Rfree = 0.000) for 3541 atoms. Found 70 (87 requested) and removed 41 (60 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.80 2.09 NCS extension: 1 residues added (12 deleted due to clashes), 3573 seeds are put forward Round 1: 362 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 2: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 3: 362 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 4: 362 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 5: 362 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Taking the results from Round 5 Chains 5, Residues 357, Estimated correctness of the model 99.8 % 5 chains (357 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 29 A 4 chains (360 residues) following loop building 4 chains (360 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3457 restraints for refining 3447 atoms. 534 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1917 (Rfree = 0.000) for 3447 atoms. Found 83 (83 requested) and removed 62 (59 requested) atoms. Cycle 22: After refmac, R = 0.1802 (Rfree = 0.000) for 3462 atoms. Found 80 (80 requested) and removed 41 (59 requested) atoms. Cycle 23: After refmac, R = 0.1712 (Rfree = 0.000) for 3497 atoms. Found 67 (79 requested) and removed 44 (59 requested) atoms. Cycle 24: After refmac, R = 0.1663 (Rfree = 0.000) for 3517 atoms. Found 69 (77 requested) and removed 38 (60 requested) atoms. Cycle 25: After refmac, R = 0.1630 (Rfree = 0.000) for 3546 atoms. Found 59 (75 requested) and removed 38 (60 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.80 2.09 NCS extension: 1 residues added (27 deleted due to clashes), 3570 seeds are put forward Round 1: 362 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 2: 362 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 3: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 4: 365 peptides, 5 chains. Longest chain 92 peptides. Score 0.965 Round 5: 363 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Taking the results from Round 4 Chains 5, Residues 360, Estimated correctness of the model 99.8 % 5 chains (360 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 C and 91 C 4 chains (362 residues) following loop building 4 chains (362 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3430 restraints for refining 3466 atoms. 486 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1890 (Rfree = 0.000) for 3466 atoms. Found 71 (71 requested) and removed 64 (59 requested) atoms. Cycle 27: After refmac, R = 0.1760 (Rfree = 0.000) for 3466 atoms. Found 68 (68 requested) and removed 36 (59 requested) atoms. Cycle 28: After refmac, R = 0.1695 (Rfree = 0.000) for 3493 atoms. Found 67 (67 requested) and removed 27 (59 requested) atoms. Cycle 29: After refmac, R = 0.1652 (Rfree = 0.000) for 3531 atoms. Found 60 (68 requested) and removed 35 (60 requested) atoms. Cycle 30: After refmac, R = 0.1627 (Rfree = 0.000) for 3553 atoms. Found 62 (65 requested) and removed 48 (60 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.80 2.09 NCS extension: 0 residues added (28 deleted due to clashes), 3571 seeds are put forward Round 1: 363 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 2: 364 peptides, 5 chains. Longest chain 92 peptides. Score 0.965 Round 3: 362 peptides, 7 chains. Longest chain 92 peptides. Score 0.958 Round 4: 364 peptides, 5 chains. Longest chain 92 peptides. Score 0.965 Round 5: 363 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Taking the results from Round 4 Chains 5, Residues 359, Estimated correctness of the model 99.8 % 4 chains (347 residues) have been docked in sequence Building loops using Loopy2018 5 chains (359 residues) following loop building 4 chains (347 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3496 restraints for refining 3462 atoms. 617 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1876 (Rfree = 0.000) for 3462 atoms. Found 61 (61 requested) and removed 61 (59 requested) atoms. Cycle 32: After refmac, R = 0.1747 (Rfree = 0.000) for 3454 atoms. Found 59 (59 requested) and removed 37 (59 requested) atoms. Cycle 33: After refmac, R = 0.1683 (Rfree = 0.000) for 3476 atoms. Found 59 (59 requested) and removed 30 (59 requested) atoms. Cycle 34: After refmac, R = 0.1643 (Rfree = 0.000) for 3503 atoms. Found 60 (60 requested) and removed 34 (60 requested) atoms. Cycle 35: After refmac, R = 0.1617 (Rfree = 0.000) for 3525 atoms. Found 60 (60 requested) and removed 31 (60 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.80 2.09 NCS extension: 2 residues added (26 deleted due to clashes), 3558 seeds are put forward Round 1: 363 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 2: 364 peptides, 5 chains. Longest chain 92 peptides. Score 0.965 Round 3: 363 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 4: 362 peptides, 7 chains. Longest chain 92 peptides. Score 0.958 Round 5: 363 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Taking the results from Round 2 Chains 5, Residues 359, Estimated correctness of the model 99.8 % 5 chains (359 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 C and 29 C 4 chains (362 residues) following loop building 4 chains (362 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3422 restraints for refining 3480 atoms. 478 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1825 (Rfree = 0.000) for 3480 atoms. Found 59 (59 requested) and removed 60 (59 requested) atoms. Cycle 37: After refmac, R = 0.1713 (Rfree = 0.000) for 3472 atoms. Found 59 (59 requested) and removed 33 (59 requested) atoms. Cycle 38: After refmac, R = 0.1656 (Rfree = 0.000) for 3494 atoms. Found 59 (59 requested) and removed 29 (59 requested) atoms. Cycle 39: After refmac, R = 0.1633 (Rfree = 0.000) for 3523 atoms. Found 60 (60 requested) and removed 43 (60 requested) atoms. Cycle 40: After refmac, R = 0.1611 (Rfree = 0.000) for 3538 atoms. Found 60 (60 requested) and removed 39 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.81 2.10 NCS extension: 0 residues added (13 deleted due to clashes), 3562 seeds are put forward Round 1: 365 peptides, 5 chains. Longest chain 92 peptides. Score 0.965 Round 2: 365 peptides, 5 chains. Longest chain 92 peptides. Score 0.965 Round 3: 365 peptides, 5 chains. Longest chain 92 peptides. Score 0.965 Round 4: 364 peptides, 6 chains. Longest chain 92 peptides. Score 0.962 Round 5: 366 peptides, 4 chains. Longest chain 92 peptides. Score 0.968 Taking the results from Round 5 Chains 4, Residues 362, Estimated correctness of the model 99.9 % 4 chains (362 residues) have been docked in sequence Building loops using Loopy2018 4 chains (362 residues) following loop building 4 chains (362 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3431 restraints for refining 3482 atoms. 487 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1844 (Rfree = 0.000) for 3482 atoms. Found 59 (59 requested) and removed 61 (59 requested) atoms. Cycle 42: After refmac, R = 0.1735 (Rfree = 0.000) for 3471 atoms. Found 59 (59 requested) and removed 41 (59 requested) atoms. Cycle 43: After refmac, R = 0.1673 (Rfree = 0.000) for 3486 atoms. Found 59 (59 requested) and removed 24 (59 requested) atoms. Cycle 44: After refmac, R = 0.1647 (Rfree = 0.000) for 3519 atoms. Found 60 (60 requested) and removed 30 (60 requested) atoms. Cycle 45: After refmac, R = 0.1614 (Rfree = 0.000) for 3547 atoms. Found 60 (60 requested) and removed 39 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.80 2.09 NCS extension: 0 residues added (13 deleted due to clashes), 3571 seeds are put forward Round 1: 366 peptides, 4 chains. Longest chain 92 peptides. Score 0.968 Round 2: 363 peptides, 7 chains. Longest chain 92 peptides. Score 0.958 Round 3: 366 peptides, 4 chains. Longest chain 92 peptides. Score 0.968 Round 4: 364 peptides, 6 chains. Longest chain 92 peptides. Score 0.962 Round 5: 364 peptides, 6 chains. Longest chain 92 peptides. Score 0.962 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 362, Estimated correctness of the model 99.9 % 4 chains (361 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 5 chains (362 residues) following loop building 4 chains (361 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 23674 reflections ( 95.48 % complete ) and 2934 restraints for refining 2893 atoms. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2463 (Rfree = 0.000) for 2893 atoms. Found 49 (49 requested) and removed 0 (49 requested) atoms. Cycle 47: After refmac, R = 0.2258 (Rfree = 0.000) for 2893 atoms. Found 46 (50 requested) and removed 1 (50 requested) atoms. Cycle 48: After refmac, R = 0.2136 (Rfree = 0.000) for 2893 atoms. Found 21 (51 requested) and removed 1 (51 requested) atoms. Cycle 49: After refmac, R = 0.2062 (Rfree = 0.000) for 2893 atoms. TimeTaking 41.6