null Tue 25 Dec 19:27:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vk8-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk8-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:11 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/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-hancs/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-hancs.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-hancs.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 3765 atoms. Observations/parameters ratio is 1.57 ------------------------------------------------------ Starting model: R = 0.2977 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2377 (Rfree = 0.000) for 3765 atoms. Found 106 (128 requested) and removed 76 (64 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.80 2.09 NCS extension: 0 residues added, 3795 seeds are put forward Round 1: 298 peptides, 22 chains. Longest chain 37 peptides. Score 0.838 Round 2: 323 peptides, 15 chains. Longest chain 51 peptides. Score 0.905 Round 3: 341 peptides, 9 chains. Longest chain 91 peptides. Score 0.942 Round 4: 340 peptides, 9 chains. Longest chain 93 peptides. Score 0.942 Round 5: 346 peptides, 9 chains. Longest chain 93 peptides. Score 0.944 Taking the results from Round 5 Chains 9, Residues 337, Estimated correctness of the model 99.6 % 5 chains (297 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 C and 30 C 8 chains (339 residues) following loop building 4 chains (299 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3740 restraints for refining 3286 atoms. 1140 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2728 (Rfree = 0.000) for 3286 atoms. Found 92 (112 requested) and removed 63 (56 requested) atoms. Cycle 2: After refmac, R = 0.2467 (Rfree = 0.000) for 3298 atoms. Found 83 (111 requested) and removed 38 (56 requested) atoms. Cycle 3: After refmac, R = 0.2216 (Rfree = 0.000) for 3333 atoms. Found 85 (112 requested) and removed 33 (57 requested) atoms. Cycle 4: After refmac, R = 0.2073 (Rfree = 0.000) for 3370 atoms. Found 78 (113 requested) and removed 19 (57 requested) atoms. Cycle 5: After refmac, R = 0.1974 (Rfree = 0.000) for 3418 atoms. Found 60 (115 requested) and removed 26 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.80 2.09 NCS extension: 7 residues added (39 deleted due to clashes), 3462 seeds are put forward Round 1: 350 peptides, 7 chains. Longest chain 92 peptides. Score 0.953 Round 2: 353 peptides, 7 chains. Longest chain 92 peptides. Score 0.954 Round 3: 355 peptides, 7 chains. Longest chain 92 peptides. Score 0.955 Round 4: 357 peptides, 6 chains. Longest chain 92 peptides. Score 0.959 Round 5: 360 peptides, 7 chains. Longest chain 91 peptides. Score 0.957 Taking the results from Round 4 Chains 6, Residues 351, Estimated correctness of the model 99.8 % 4 chains (329 residues) have been docked in sequence Building loops using Loopy2018 6 chains (351 residues) following loop building 4 chains (329 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3639 restraints for refining 3382 atoms. 856 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2096 (Rfree = 0.000) for 3382 atoms. Found 113 (113 requested) and removed 65 (57 requested) atoms. Cycle 7: After refmac, R = 0.1973 (Rfree = 0.000) for 3423 atoms. Found 94 (112 requested) and removed 50 (58 requested) atoms. Cycle 8: After refmac, R = 0.1878 (Rfree = 0.000) for 3465 atoms. Found 74 (111 requested) and removed 34 (59 requested) atoms. Cycle 9: After refmac, R = 0.1815 (Rfree = 0.000) for 3499 atoms. Found 73 (113 requested) and removed 38 (60 requested) atoms. Cycle 10: After refmac, R = 0.1763 (Rfree = 0.000) for 3528 atoms. Found 73 (111 requested) and removed 38 (60 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.81 2.10 NCS extension: 6 residues added (28 deleted due to clashes), 3572 seeds are put forward Round 1: 361 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 2: 363 peptides, 5 chains. Longest chain 93 peptides. Score 0.964 Round 3: 361 peptides, 7 chains. Longest chain 93 peptides. Score 0.957 Round 4: 360 peptides, 7 chains. Longest chain 92 peptides. Score 0.957 Round 5: 361 peptides, 8 chains. Longest chain 77 peptides. Score 0.954 Taking the results from Round 2 Chains 5, Residues 358, Estimated correctness of the model 99.8 % 4 chains (346 residues) have been docked in sequence Building loops using Loopy2018 5 chains (358 residues) following loop building 4 chains (346 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3563 restraints for refining 3472 atoms. 688 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1973 (Rfree = 0.000) for 3472 atoms. Found 96 (106 requested) and removed 65 (59 requested) atoms. Cycle 12: After refmac, R = 0.1838 (Rfree = 0.000) for 3493 atoms. Found 63 (106 requested) and removed 38 (60 requested) atoms. Cycle 13: After refmac, R = 0.1767 (Rfree = 0.000) for 3514 atoms. Found 66 (103 requested) and removed 33 (60 requested) atoms. Cycle 14: After refmac, R = 0.1717 (Rfree = 0.000) for 3545 atoms. Found 55 (104 requested) and removed 38 (60 requested) atoms. Cycle 15: After refmac, R = 0.1685 (Rfree = 0.000) for 3555 atoms. Found 58 (102 requested) and removed 38 (61 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.81 2.10 NCS extension: 2 residues added (13 deleted due to clashes), 3577 seeds are put forward Round 1: 362 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 2: 362 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 3: 365 peptides, 4 chains. Longest chain 93 peptides. Score 0.968 Round 4: 364 peptides, 5 chains. Longest chain 93 peptides. Score 0.965 Round 5: 364 peptides, 5 chains. Longest chain 93 peptides. Score 0.965 Taking the results from Round 3 Chains 4, Residues 361, Estimated correctness of the model 99.9 % 4 chains (361 residues) have been docked in sequence Building loops using Loopy2018 4 chains (361 residues) following loop building 4 chains (361 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3472 restraints for refining 3498 atoms. 536 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1928 (Rfree = 0.000) for 3498 atoms. Found 98 (98 requested) and removed 64 (59 requested) atoms. Cycle 17: After refmac, R = 0.1804 (Rfree = 0.000) for 3521 atoms. Found 83 (96 requested) and removed 61 (60 requested) atoms. Cycle 18: After refmac, R = 0.1750 (Rfree = 0.000) for 3537 atoms. Found 68 (94 requested) and removed 44 (60 requested) atoms. Cycle 19: After refmac, R = 0.1710 (Rfree = 0.000) for 3559 atoms. Found 76 (92 requested) and removed 33 (60 requested) atoms. Cycle 20: After refmac, R = 0.1675 (Rfree = 0.000) for 3599 atoms. Found 63 (93 requested) and removed 48 (61 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.80 2.09 NCS extension: 0 residues added (14 deleted due to clashes), 3615 seeds are put forward Round 1: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 2: 363 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 3: 364 peptides, 5 chains. Longest chain 93 peptides. Score 0.965 Round 4: 362 peptides, 7 chains. Longest chain 93 peptides. Score 0.958 Round 5: 364 peptides, 5 chains. Longest chain 93 peptides. Score 0.965 Taking the results from Round 5 Chains 5, Residues 359, Estimated correctness of the model 99.8 % 4 chains (348 residues) have been docked in sequence Building loops using Loopy2018 5 chains (359 residues) following loop building 4 chains (348 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3582 restraints for refining 3495 atoms. 698 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1891 (Rfree = 0.000) for 3495 atoms. Found 88 (88 requested) and removed 62 (59 requested) atoms. Cycle 22: After refmac, R = 0.1778 (Rfree = 0.000) for 3507 atoms. Found 66 (86 requested) and removed 38 (60 requested) atoms. Cycle 23: After refmac, R = 0.1723 (Rfree = 0.000) for 3528 atoms. Found 68 (85 requested) and removed 40 (60 requested) atoms. Cycle 24: After refmac, R = 0.1680 (Rfree = 0.000) for 3551 atoms. Found 82 (82 requested) and removed 27 (60 requested) atoms. Cycle 25: After refmac, R = 0.1659 (Rfree = 0.000) for 3604 atoms. Found 60 (84 requested) and removed 55 (61 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.81 2.10 NCS extension: 2 residues added (27 deleted due to clashes), 3612 seeds are put forward Round 1: 364 peptides, 5 chains. Longest chain 91 peptides. Score 0.965 Round 2: 364 peptides, 6 chains. Longest chain 93 peptides. Score 0.962 Round 3: 364 peptides, 6 chains. Longest chain 93 peptides. Score 0.962 Round 4: 364 peptides, 6 chains. Longest chain 93 peptides. Score 0.962 Round 5: 363 peptides, 7 chains. Longest chain 92 peptides. Score 0.958 Taking the results from Round 1 Chains 6, Residues 359, Estimated correctness of the model 99.8 % 5 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 D and 33 D 5 chains (361 residues) following loop building 4 chains (360 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3458 restraints for refining 3508 atoms. 532 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1877 (Rfree = 0.000) for 3508 atoms. Found 79 (79 requested) and removed 63 (60 requested) atoms. Cycle 27: After refmac, R = 0.1751 (Rfree = 0.000) for 3514 atoms. Found 77 (77 requested) and removed 40 (60 requested) atoms. Cycle 28: After refmac, R = 0.1697 (Rfree = 0.000) for 3542 atoms. Found 65 (75 requested) and removed 24 (60 requested) atoms. Cycle 29: After refmac, R = 0.1650 (Rfree = 0.000) for 3582 atoms. Found 60 (76 requested) and removed 41 (61 requested) atoms. Cycle 30: After refmac, R = 0.1620 (Rfree = 0.000) for 3599 atoms. Found 57 (74 requested) and removed 36 (61 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.79 2.08 NCS extension: 0 residues added (29 deleted due to clashes), 3622 seeds are put forward Round 1: 361 peptides, 7 chains. Longest chain 90 peptides. Score 0.957 Round 2: 363 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 3: 365 peptides, 5 chains. Longest chain 94 peptides. Score 0.965 Round 4: 363 peptides, 6 chains. Longest chain 94 peptides. Score 0.961 Round 5: 364 peptides, 6 chains. Longest chain 94 peptides. Score 0.962 Taking the results from Round 3 Chains 6, Residues 360, Estimated correctness of the model 99.8 % 4 chains (346 residues) have been docked in sequence Building loops using Loopy2018 6 chains (360 residues) following loop building 4 chains (346 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3551 restraints for refining 3490 atoms. 674 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1877 (Rfree = 0.000) for 3490 atoms. Found 69 (69 requested) and removed 61 (59 requested) atoms. Cycle 32: After refmac, R = 0.1765 (Rfree = 0.000) for 3489 atoms. Found 67 (67 requested) and removed 35 (59 requested) atoms. Cycle 33: After refmac, R = 0.1690 (Rfree = 0.000) for 3519 atoms. Found 65 (65 requested) and removed 36 (60 requested) atoms. Cycle 34: After refmac, R = 0.1661 (Rfree = 0.000) for 3547 atoms. Found 63 (63 requested) and removed 38 (60 requested) atoms. Cycle 35: After refmac, R = 0.1640 (Rfree = 0.000) for 3570 atoms. Found 61 (61 requested) and removed 44 (61 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.79 2.08 NCS extension: 2 residues added (41 deleted due to clashes), 3592 seeds are put forward Round 1: 362 peptides, 7 chains. Longest chain 93 peptides. Score 0.958 Round 2: 362 peptides, 7 chains. Longest chain 93 peptides. Score 0.958 Round 3: 362 peptides, 7 chains. Longest chain 93 peptides. Score 0.958 Round 4: 362 peptides, 7 chains. Longest chain 93 peptides. Score 0.958 Round 5: 361 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Taking the results from Round 5 Chains 6, Residues 355, Estimated correctness of the model 99.8 % 5 chains (345 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 30 A 5 chains (358 residues) following loop building 4 chains (348 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3540 restraints for refining 3465 atoms. 660 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1907 (Rfree = 0.000) for 3465 atoms. Found 59 (59 requested) and removed 63 (59 requested) atoms. Cycle 37: After refmac, R = 0.1758 (Rfree = 0.000) for 3450 atoms. Found 59 (59 requested) and removed 22 (59 requested) atoms. Cycle 38: After refmac, R = 0.1687 (Rfree = 0.000) for 3486 atoms. Found 59 (59 requested) and removed 27 (59 requested) atoms. Cycle 39: After refmac, R = 0.1647 (Rfree = 0.000) for 3516 atoms. Found 60 (60 requested) and removed 36 (60 requested) atoms. Cycle 40: After refmac, R = 0.1626 (Rfree = 0.000) for 3540 atoms. Found 58 (60 requested) and removed 43 (60 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.80 2.09 NCS extension: 2 residues added (12 deleted due to clashes), 3560 seeds are put forward Round 1: 362 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 2: 364 peptides, 5 chains. Longest chain 93 peptides. Score 0.965 Round 3: 360 peptides, 8 chains. Longest chain 92 peptides. Score 0.954 Round 4: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 5: 361 peptides, 6 chains. Longest chain 93 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 26 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 3425 restraints for refining 3476 atoms. 480 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1859 (Rfree = 0.000) for 3476 atoms. Found 59 (59 requested) and removed 62 (59 requested) atoms. Cycle 42: After refmac, R = 0.1749 (Rfree = 0.000) for 3466 atoms. Found 59 (59 requested) and removed 39 (59 requested) atoms. Cycle 43: After refmac, R = 0.1687 (Rfree = 0.000) for 3485 atoms. Found 59 (59 requested) and removed 26 (59 requested) atoms. Cycle 44: After refmac, R = 0.1659 (Rfree = 0.000) for 3517 atoms. Found 60 (60 requested) and removed 33 (60 requested) atoms. Cycle 45: After refmac, R = 0.1628 (Rfree = 0.000) for 3542 atoms. Found 58 (60 requested) and removed 34 (60 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.80 2.09 NCS extension: 0 residues added (14 deleted due to clashes), 3568 seeds are put forward Round 1: 360 peptides, 6 chains. Longest chain 92 peptides. Score 0.960 Round 2: 361 peptides, 8 chains. Longest chain 93 peptides. Score 0.954 Round 3: 364 peptides, 4 chains. Longest chain 92 peptides. Score 0.968 Round 4: 359 peptides, 8 chains. Longest chain 92 peptides. Score 0.953 Round 5: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 360, Estimated correctness of the model 99.9 % 4 chains (360 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 4 chains (360 residues) following loop building 4 chains (360 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 23674 reflections ( 95.48 % complete ) and 2923 restraints for refining 2882 atoms. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2469 (Rfree = 0.000) for 2882 atoms. Found 49 (49 requested) and removed 0 (49 requested) atoms. Cycle 47: After refmac, R = 0.2277 (Rfree = 0.000) for 2882 atoms. Found 40 (50 requested) and removed 0 (50 requested) atoms. Cycle 48: After refmac, R = 0.2155 (Rfree = 0.000) for 2882 atoms. Found 20 (50 requested) and removed 1 (50 requested) atoms. Cycle 49: After refmac, R = 0.2089 (Rfree = 0.000) for 2882 atoms. Found 14 (51 requested) and removed 2 (51 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:41:27 GMT 2018 Job finished. TimeTaking 73.53 Used memory is bytes: 8278624