Mon 24 Dec 07:29:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vk8-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vk8-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-noncs ############### 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 07:29:58 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/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vk8-2.0-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.45 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 3760 atoms. Observations/parameters ratio is 1.57 ------------------------------------------------------ Starting model: R = 0.3242 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2681 (Rfree = 0.000) for 3760 atoms. Found 84 (128 requested) and removed 74 (64 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.79 2.08 NCS extension: 0 residues added, 3770 seeds are put forward Round 1: 241 peptides, 31 chains. Longest chain 23 peptides. Score 0.635 Round 2: 285 peptides, 24 chains. Longest chain 30 peptides. Score 0.804 Round 3: 306 peptides, 19 chains. Longest chain 50 peptides. Score 0.868 Round 4: 319 peptides, 13 chains. Longest chain 67 peptides. Score 0.912 Round 5: 318 peptides, 15 chains. Longest chain 67 peptides. Score 0.901 Taking the results from Round 4 Chains 13, Residues 306, Estimated correctness of the model 99.2 % 5 chains (233 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 C and 72 C 12 chains (308 residues) following loop building 4 chains (235 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 4149 restraints for refining 3288 atoms. 1915 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3078 (Rfree = 0.000) for 3288 atoms. Found 106 (112 requested) and removed 57 (56 requested) atoms. Cycle 2: After refmac, R = 0.2886 (Rfree = 0.000) for 3325 atoms. Found 84 (112 requested) and removed 58 (57 requested) atoms. Cycle 3: After refmac, R = 0.2640 (Rfree = 0.000) for 3340 atoms. Found 61 (109 requested) and removed 46 (57 requested) atoms. Cycle 4: After refmac, R = 0.2474 (Rfree = 0.000) for 3332 atoms. Found 90 (107 requested) and removed 31 (57 requested) atoms. Cycle 5: After refmac, R = 0.2360 (Rfree = 0.000) for 3377 atoms. Found 75 (109 requested) and removed 18 (58 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.79 2.08 NCS extension: 2 residues added (32 deleted due to clashes), 3441 seeds are put forward Round 1: 324 peptides, 10 chains. Longest chain 73 peptides. Score 0.929 Round 2: 331 peptides, 10 chains. Longest chain 73 peptides. Score 0.933 Round 3: 332 peptides, 9 chains. Longest chain 74 peptides. Score 0.937 Round 4: 330 peptides, 11 chains. Longest chain 70 peptides. Score 0.928 Round 5: 332 peptides, 9 chains. Longest chain 72 peptides. Score 0.937 Taking the results from Round 5 Chains 9, Residues 323, Estimated correctness of the model 99.6 % 4 chains (264 residues) have been docked in sequence Building loops using Loopy2018 9 chains (323 residues) following loop building 4 chains (264 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3825 restraints for refining 3301 atoms. 1419 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2459 (Rfree = 0.000) for 3301 atoms. Found 106 (106 requested) and removed 58 (56 requested) atoms. Cycle 7: After refmac, R = 0.2286 (Rfree = 0.000) for 3342 atoms. Found 66 (105 requested) and removed 29 (57 requested) atoms. Cycle 8: After refmac, R = 0.2158 (Rfree = 0.000) for 3375 atoms. Found 65 (106 requested) and removed 21 (57 requested) atoms. Cycle 9: After refmac, R = 0.2054 (Rfree = 0.000) for 3418 atoms. Found 52 (108 requested) and removed 19 (58 requested) atoms. Cycle 10: After refmac, R = 0.1981 (Rfree = 0.000) for 3445 atoms. Found 50 (109 requested) and removed 19 (59 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.81 2.10 NCS extension: 0 residues added (15 deleted due to clashes), 3477 seeds are put forward Round 1: 334 peptides, 9 chains. Longest chain 75 peptides. Score 0.938 Round 2: 333 peptides, 9 chains. Longest chain 70 peptides. Score 0.938 Round 3: 335 peptides, 8 chains. Longest chain 91 peptides. Score 0.943 Round 4: 336 peptides, 9 chains. Longest chain 70 peptides. Score 0.939 Round 5: 338 peptides, 7 chains. Longest chain 91 peptides. Score 0.948 Taking the results from Round 5 Chains 7, Residues 331, Estimated correctness of the model 99.7 % 4 chains (298 residues) have been docked in sequence Building loops using Loopy2018 7 chains (331 residues) following loop building 4 chains (298 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3687 restraints for refining 3390 atoms. 1113 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2186 (Rfree = 0.000) for 3390 atoms. Found 94 (107 requested) and removed 61 (58 requested) atoms. Cycle 12: After refmac, R = 0.2052 (Rfree = 0.000) for 3416 atoms. Found 83 (105 requested) and removed 29 (58 requested) atoms. Cycle 13: After refmac, R = 0.1947 (Rfree = 0.000) for 3468 atoms. Found 49 (106 requested) and removed 20 (59 requested) atoms. Cycle 14: After refmac, R = 0.1891 (Rfree = 0.000) for 3486 atoms. Found 50 (107 requested) and removed 23 (59 requested) atoms. Cycle 15: After refmac, R = 0.1836 (Rfree = 0.000) for 3511 atoms. Found 43 (108 requested) and removed 22 (60 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.80 2.09 NCS extension: 4 residues added (17 deleted due to clashes), 3538 seeds are put forward Round 1: 333 peptides, 8 chains. Longest chain 91 peptides. Score 0.942 Round 2: 340 peptides, 7 chains. Longest chain 92 peptides. Score 0.949 Round 3: 340 peptides, 8 chains. Longest chain 93 peptides. Score 0.945 Round 4: 340 peptides, 8 chains. Longest chain 78 peptides. Score 0.945 Round 5: 338 peptides, 10 chains. Longest chain 93 peptides. Score 0.937 Taking the results from Round 2 Chains 7, Residues 333, Estimated correctness of the model 99.7 % 5 chains (310 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 D and 34 D 6 chains (341 residues) following loop building 4 chains (318 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 23674 reflections ( 95.48 % complete ) and 3707 restraints for refining 3467 atoms. 1016 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2116 (Rfree = 0.000) for 3467 atoms. Found 104 (104 requested) and removed 63 (59 requested) atoms. Cycle 17: After refmac, R = 0.1959 (Rfree = 0.000) for 3500 atoms. Found 69 (103 requested) and removed 47 (60 requested) atoms. Cycle 18: After refmac, R = 0.1873 (Rfree = 0.000) for 3513 atoms. Found 63 (101 requested) and removed 26 (60 requested) atoms. Cycle 19: After refmac, R = 0.1820 (Rfree = 0.000) for 3542 atoms. Found 52 (102 requested) and removed 26 (60 requested) atoms. Cycle 20: After refmac, R = 0.1765 (Rfree = 0.000) for 3563 atoms. Found 50 (102 requested) and removed 22 (61 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.82 2.11 NCS extension: 8 residues added (33 deleted due to clashes), 3603 seeds are put forward Round 1: 340 peptides, 7 chains. Longest chain 92 peptides. Score 0.949 Round 2: 340 peptides, 8 chains. Longest chain 93 peptides. Score 0.945 Round 3: 342 peptides, 7 chains. Longest chain 93 peptides. Score 0.950 Round 4: 342 peptides, 8 chains. Longest chain 93 peptides. Score 0.946 Round 5: 341 peptides, 8 chains. Longest chain 93 peptides. Score 0.946 Taking the results from Round 3 Chains 7, Residues 335, Estimated correctness of the model 99.7 % 5 chains (312 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 D and 34 D 6 chains (343 residues) following loop building 4 chains (320 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3689 restraints for refining 3482 atoms. 978 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2012 (Rfree = 0.000) for 3482 atoms. Found 100 (100 requested) and removed 61 (59 requested) atoms. Cycle 22: After refmac, R = 0.1893 (Rfree = 0.000) for 3504 atoms. Found 59 (98 requested) and removed 30 (60 requested) atoms. Cycle 23: After refmac, R = 0.1814 (Rfree = 0.000) for 3527 atoms. Found 69 (97 requested) and removed 15 (60 requested) atoms. Cycle 24: After refmac, R = 0.1748 (Rfree = 0.000) for 3575 atoms. Found 60 (98 requested) and removed 22 (61 requested) atoms. Cycle 25: After refmac, R = 0.1698 (Rfree = 0.000) for 3607 atoms. Found 61 (98 requested) and removed 34 (61 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.79 2.08 NCS extension: 9 residues added (34 deleted due to clashes), 3644 seeds are put forward Round 1: 346 peptides, 7 chains. Longest chain 92 peptides. Score 0.951 Round 2: 347 peptides, 8 chains. Longest chain 92 peptides. Score 0.948 Round 3: 350 peptides, 8 chains. Longest chain 78 peptides. Score 0.950 Round 4: 351 peptides, 7 chains. Longest chain 93 peptides. Score 0.954 Round 5: 349 peptides, 10 chains. Longest chain 76 peptides. Score 0.942 Taking the results from Round 4 Chains 7, Residues 344, Estimated correctness of the model 99.7 % 6 chains (333 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 30 A Built loop between residues 26 D and 30 D 5 chains (351 residues) following loop building 4 chains (340 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3554 restraints for refining 3497 atoms. 737 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1958 (Rfree = 0.000) for 3497 atoms. Found 93 (93 requested) and removed 63 (59 requested) atoms. Cycle 27: After refmac, R = 0.1988 (Rfree = 0.000) for 3517 atoms. Found 91 (91 requested) and removed 59 (60 requested) atoms. Cycle 28: After refmac, R = 0.1901 (Rfree = 0.000) for 3543 atoms. Found 90 (90 requested) and removed 29 (60 requested) atoms. Cycle 29: After refmac, R = 0.1815 (Rfree = 0.000) for 3591 atoms. Found 71 (91 requested) and removed 27 (61 requested) atoms. Cycle 30: After refmac, R = 0.1746 (Rfree = 0.000) for 3623 atoms. Found 71 (92 requested) and removed 37 (62 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.79 2.08 NCS extension: 11 residues added (27 deleted due to clashes), 3671 seeds are put forward Round 1: 356 peptides, 7 chains. Longest chain 92 peptides. Score 0.956 Round 2: 358 peptides, 6 chains. Longest chain 92 peptides. Score 0.959 Round 3: 359 peptides, 6 chains. Longest chain 92 peptides. Score 0.960 Round 4: 359 peptides, 6 chains. Longest chain 92 peptides. Score 0.960 Round 5: 357 peptides, 8 chains. Longest chain 92 peptides. Score 0.953 Taking the results from Round 4 Chains 6, Residues 353, Estimated correctness of the model 99.8 % 5 chains (341 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 25 A and 30 A 5 chains (357 residues) following loop building 4 chains (345 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3558 restraints for refining 3512 atoms. 701 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1958 (Rfree = 0.000) for 3512 atoms. Found 86 (86 requested) and removed 61 (60 requested) atoms. Cycle 32: After refmac, R = 0.1823 (Rfree = 0.000) for 3528 atoms. Found 85 (85 requested) and removed 38 (60 requested) atoms. Cycle 33: After refmac, R = 0.1746 (Rfree = 0.000) for 3571 atoms. Found 85 (85 requested) and removed 33 (61 requested) atoms. Cycle 34: After refmac, R = 0.1706 (Rfree = 0.000) for 3620 atoms. Found 76 (87 requested) and removed 43 (62 requested) atoms. Cycle 35: After refmac, R = 0.1658 (Rfree = 0.000) for 3648 atoms. Found 84 (85 requested) and removed 48 (62 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.79 2.08 NCS extension: 2 residues added (13 deleted due to clashes), 3687 seeds are put forward Round 1: 359 peptides, 7 chains. Longest chain 93 peptides. Score 0.957 Round 2: 359 peptides, 7 chains. Longest chain 93 peptides. Score 0.957 Round 3: 360 peptides, 7 chains. Longest chain 93 peptides. Score 0.957 Round 4: 361 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 5: 359 peptides, 9 chains. Longest chain 77 peptides. Score 0.950 Taking the results from Round 4 Chains 6, Residues 355, Estimated correctness of the model 99.8 % 6 chains (355 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 C and 30 C Built loop between residues 76 C and 79 C 4 chains (360 residues) following loop building 4 chains (360 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3468 restraints for refining 3530 atoms. 541 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1906 (Rfree = 0.000) for 3530 atoms. Found 79 (79 requested) and removed 64 (60 requested) atoms. Cycle 37: After refmac, R = 0.1795 (Rfree = 0.000) for 3537 atoms. Found 77 (77 requested) and removed 44 (60 requested) atoms. Cycle 38: After refmac, R = 0.1715 (Rfree = 0.000) for 3567 atoms. Found 76 (76 requested) and removed 29 (61 requested) atoms. Cycle 39: After refmac, R = 0.1657 (Rfree = 0.000) for 3612 atoms. Found 59 (76 requested) and removed 39 (61 requested) atoms. Cycle 40: After refmac, R = 0.1620 (Rfree = 0.000) for 3629 atoms. Found 74 (74 requested) and removed 37 (62 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.79 2.08 NCS extension: 1 residues added (12 deleted due to clashes), 3668 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: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 4: 363 peptides, 6 chains. Longest chain 93 peptides. Score 0.961 Round 5: 362 peptides, 7 chains. Longest chain 93 peptides. Score 0.958 Taking the results from Round 3 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 59 C and 62 C 4 chains (360 residues) following loop building 4 chains (360 residues) in sequence following loop building ------------------------------------------------------ 23674 reflections ( 95.48 % complete ) and 3443 restraints for refining 3529 atoms. 520 conditional restraints added. Observations/parameters ratio is 1.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1881 (Rfree = 0.000) for 3529 atoms. Found 72 (72 requested) and removed 65 (60 requested) atoms. Cycle 42: After refmac, R = 0.1762 (Rfree = 0.000) for 3529 atoms. Found 70 (70 requested) and removed 39 (60 requested) atoms. Cycle 43: After refmac, R = 0.1693 (Rfree = 0.000) for 3559 atoms. Found 68 (68 requested) and removed 34 (60 requested) atoms. Cycle 44: After refmac, R = 0.1639 (Rfree = 0.000) for 3592 atoms. Found 69 (69 requested) and removed 32 (61 requested) atoms. Cycle 45: After refmac, R = 0.1620 (Rfree = 0.000) for 3626 atoms. Found 65 (69 requested) and removed 47 (62 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.80 2.09 NCS extension: 0 residues added (14 deleted due to clashes), 3646 seeds are put forward Round 1: 363 peptides, 5 chains. Longest chain 92 peptides. Score 0.964 Round 2: 361 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 3: 361 peptides, 7 chains. Longest chain 92 peptides. Score 0.957 Round 4: 362 peptides, 6 chains. Longest chain 92 peptides. Score 0.961 Round 5: 364 peptides, 5 chains. Longest chain 93 peptides. Score 0.965 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 359, Estimated correctness of the model 99.8 % 5 chains (359 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 26 A and 29 A 4 chains (361 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 2936 restraints for refining 2894 atoms. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2507 (Rfree = 0.000) for 2894 atoms. Found 53 (53 requested) and removed 0 (53 requested) atoms. Cycle 47: After refmac, R = 0.2311 (Rfree = 0.000) for 2894 atoms. Found 26 (54 requested) and removed 0 (50 requested) atoms. Cycle 48: After refmac, R = 0.2201 (Rfree = 0.000) for 2894 atoms. Found 20 (55 requested) and removed 0 (50 requested) atoms. Cycle 49: After refmac, R = 0.2129 (Rfree = 0.000) for 2894 atoms. TimeTaking 45.7