Mon 24 Dec 07:52:24 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 2i5i-1.7-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-1.7-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-1.7-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-1.7-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/2i5i-1.7-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-1.7-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 07:52:29 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/2i5i-1.7-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-1.7-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 525 and 0 Target number of residues in the AU: 525 Target solvent content: 0.4948 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-1.7-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-1.7-parrot-noncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.50 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: 29.446 1.701 Wilson plot Bfac: 22.43 59787 reflections ( 99.90 % complete ) and 0 restraints for refining 4645 atoms. Observations/parameters ratio is 3.22 ------------------------------------------------------ Starting model: R = 0.3640 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3268 (Rfree = 0.000) for 4645 atoms. Found 113 (251 requested) and removed 129 (125 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.15 2.18 NCS extension: 0 residues added, 4629 seeds are put forward Round 1: 280 peptides, 54 chains. Longest chain 15 peptides. Score 0.365 Round 2: 307 peptides, 47 chains. Longest chain 18 peptides. Score 0.515 Round 3: 318 peptides, 43 chains. Longest chain 21 peptides. Score 0.581 Round 4: 330 peptides, 38 chains. Longest chain 22 peptides. Score 0.651 Round 5: 340 peptides, 40 chains. Longest chain 23 peptides. Score 0.653 Taking the results from Round 5 Chains 42, Residues 300, Estimated correctness of the model 93.9 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 8148 restraints for refining 4195 atoms. 6833 conditional restraints added. Observations/parameters ratio is 3.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3446 (Rfree = 0.000) for 4195 atoms. Found 136 (227 requested) and removed 69 (113 requested) atoms. Cycle 2: After refmac, R = 0.3233 (Rfree = 0.000) for 4252 atoms. Found 119 (231 requested) and removed 22 (115 requested) atoms. Cycle 3: After refmac, R = 0.3070 (Rfree = 0.000) for 4339 atoms. Found 79 (236 requested) and removed 15 (118 requested) atoms. Cycle 4: After refmac, R = 0.2958 (Rfree = 0.000) for 4399 atoms. Found 62 (239 requested) and removed 15 (119 requested) atoms. Cycle 5: After refmac, R = 0.2862 (Rfree = 0.000) for 4443 atoms. Found 66 (241 requested) and removed 9 (120 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.04 2.07 NCS extension: 10 residues added (6 deleted due to clashes), 4543 seeds are put forward Round 1: 336 peptides, 45 chains. Longest chain 23 peptides. Score 0.600 Round 2: 357 peptides, 38 chains. Longest chain 29 peptides. Score 0.699 Round 3: 351 peptides, 38 chains. Longest chain 29 peptides. Score 0.689 Round 4: 363 peptides, 32 chains. Longest chain 30 peptides. Score 0.752 Round 5: 366 peptides, 34 chains. Longest chain 29 peptides. Score 0.742 Taking the results from Round 4 Chains 38, Residues 331, Estimated correctness of the model 96.7 % 5 chains (70 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 52 A 36 chains (337 residues) following loop building 4 chains (80 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 7906 restraints for refining 4400 atoms. 6305 conditional restraints added. Observations/parameters ratio is 3.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3127 (Rfree = 0.000) for 4400 atoms. Found 157 (239 requested) and removed 67 (119 requested) atoms. Cycle 7: After refmac, R = 0.2947 (Rfree = 0.000) for 4480 atoms. Found 101 (243 requested) and removed 23 (121 requested) atoms. Cycle 8: After refmac, R = 0.2834 (Rfree = 0.000) for 4552 atoms. Found 65 (247 requested) and removed 13 (123 requested) atoms. Cycle 9: After refmac, R = 0.2763 (Rfree = 0.000) for 4595 atoms. Found 77 (249 requested) and removed 10 (124 requested) atoms. Cycle 10: After refmac, R = 0.2701 (Rfree = 0.000) for 4653 atoms. Found 55 (252 requested) and removed 9 (126 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.02 2.05 NCS extension: 24 residues added (7 deleted due to clashes), 4740 seeds are put forward Round 1: 344 peptides, 33 chains. Longest chain 29 peptides. Score 0.716 Round 2: 347 peptides, 31 chains. Longest chain 42 peptides. Score 0.735 Round 3: 350 peptides, 32 chains. Longest chain 37 peptides. Score 0.733 Round 4: 359 peptides, 33 chains. Longest chain 33 peptides. Score 0.739 Round 5: 344 peptides, 34 chains. Longest chain 42 peptides. Score 0.708 Taking the results from Round 4 Chains 36, Residues 326, Estimated correctness of the model 96.4 % 4 chains (96 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 86 A 34 chains (329 residues) following loop building 3 chains (106 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 8065 restraints for refining 4659 atoms. 6340 conditional restraints added. Observations/parameters ratio is 3.21 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2967 (Rfree = 0.000) for 4659 atoms. Found 159 (253 requested) and removed 75 (126 requested) atoms. Cycle 12: After refmac, R = 0.2815 (Rfree = 0.000) for 4740 atoms. Found 101 (257 requested) and removed 21 (128 requested) atoms. Cycle 13: After refmac, R = 0.2722 (Rfree = 0.000) for 4817 atoms. Found 83 (261 requested) and removed 19 (130 requested) atoms. Cycle 14: After refmac, R = 0.2641 (Rfree = 0.000) for 4874 atoms. Found 72 (265 requested) and removed 18 (132 requested) atoms. Cycle 15: After refmac, R = 0.2595 (Rfree = 0.000) for 4920 atoms. Found 72 (267 requested) and removed 15 (133 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.03 2.06 NCS extension: 29 residues added (12 deleted due to clashes), 5022 seeds are put forward Round 1: 354 peptides, 35 chains. Longest chain 23 peptides. Score 0.717 Round 2: 366 peptides, 34 chains. Longest chain 32 peptides. Score 0.742 Round 3: 369 peptides, 33 chains. Longest chain 30 peptides. Score 0.753 Round 4: 374 peptides, 35 chains. Longest chain 32 peptides. Score 0.747 Round 5: 365 peptides, 34 chains. Longest chain 34 peptides. Score 0.741 Taking the results from Round 3 Chains 36, Residues 336, Estimated correctness of the model 96.7 % 4 chains (88 residues) have been docked in sequence Building loops using Loopy2018 36 chains (336 residues) following loop building 4 chains (88 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 8643 restraints for refining 4856 atoms. 6978 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2812 (Rfree = 0.000) for 4856 atoms. Found 162 (263 requested) and removed 61 (131 requested) atoms. Cycle 17: After refmac, R = 0.2661 (Rfree = 0.000) for 4957 atoms. Found 89 (269 requested) and removed 20 (134 requested) atoms. Cycle 18: After refmac, R = 0.2561 (Rfree = 0.000) for 5021 atoms. Found 78 (272 requested) and removed 9 (136 requested) atoms. Cycle 19: After refmac, R = 0.2488 (Rfree = 0.000) for 5086 atoms. Found 61 (276 requested) and removed 9 (138 requested) atoms. Cycle 20: After refmac, R = 0.2439 (Rfree = 0.000) for 5133 atoms. Found 72 (278 requested) and removed 12 (139 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.01 2.04 NCS extension: 3 residues added (13 deleted due to clashes), 5208 seeds are put forward Round 1: 365 peptides, 39 chains. Longest chain 23 peptides. Score 0.705 Round 2: 365 peptides, 34 chains. Longest chain 31 peptides. Score 0.741 Round 3: 375 peptides, 34 chains. Longest chain 27 peptides. Score 0.755 Round 4: 370 peptides, 32 chains. Longest chain 32 peptides. Score 0.761 Round 5: 368 peptides, 33 chains. Longest chain 32 peptides. Score 0.752 Taking the results from Round 4 Chains 37, Residues 338, Estimated correctness of the model 96.9 % 3 chains (51 residues) have been docked in sequence Building loops using Loopy2018 37 chains (338 residues) following loop building 3 chains (51 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 9391 restraints for refining 4962 atoms. 7871 conditional restraints added. Observations/parameters ratio is 3.01 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2652 (Rfree = 0.000) for 4962 atoms. Found 192 (269 requested) and removed 32 (134 requested) atoms. Cycle 22: After refmac, R = 0.2510 (Rfree = 0.000) for 5119 atoms. Found 119 (277 requested) and removed 12 (138 requested) atoms. Cycle 23: After refmac, R = 0.2422 (Rfree = 0.000) for 5221 atoms. Found 104 (283 requested) and removed 10 (141 requested) atoms. Cycle 24: After refmac, R = 0.2363 (Rfree = 0.000) for 5309 atoms. Found 90 (288 requested) and removed 16 (144 requested) atoms. Cycle 25: After refmac, R = 0.2317 (Rfree = 0.000) for 5378 atoms. Found 73 (291 requested) and removed 23 (145 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.00 2.03 NCS extension: 11 residues added (10 deleted due to clashes), 5450 seeds are put forward Round 1: 360 peptides, 41 chains. Longest chain 30 peptides. Score 0.681 Round 2: 371 peptides, 31 chains. Longest chain 32 peptides. Score 0.769 Round 3: 373 peptides, 35 chains. Longest chain 31 peptides. Score 0.745 Round 4: 376 peptides, 32 chains. Longest chain 32 peptides. Score 0.769 Round 5: 372 peptides, 32 chains. Longest chain 30 peptides. Score 0.764 Taking the results from Round 4 Chains 34, Residues 344, Estimated correctness of the model 97.1 % 2 chains (40 residues) have been docked in sequence Building loops using Loopy2018 34 chains (344 residues) following loop building 2 chains (40 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 10183 restraints for refining 5172 atoms. 8688 conditional restraints added. Observations/parameters ratio is 2.89 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2556 (Rfree = 0.000) for 5172 atoms. Found 214 (281 requested) and removed 25 (140 requested) atoms. Cycle 27: After refmac, R = 0.2404 (Rfree = 0.000) for 5361 atoms. Found 148 (291 requested) and removed 10 (145 requested) atoms. Cycle 28: After refmac, R = 0.2337 (Rfree = 0.000) for 5492 atoms. Found 106 (298 requested) and removed 25 (149 requested) atoms. Cycle 29: After refmac, R = 0.2284 (Rfree = 0.000) for 5569 atoms. Found 110 (302 requested) and removed 27 (151 requested) atoms. Cycle 30: After refmac, R = 0.2244 (Rfree = 0.000) for 5647 atoms. Found 118 (306 requested) and removed 38 (153 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.00 2.03 NCS extension: 12 residues added (2 deleted due to clashes), 5752 seeds are put forward Round 1: 365 peptides, 35 chains. Longest chain 29 peptides. Score 0.734 Round 2: 368 peptides, 34 chains. Longest chain 32 peptides. Score 0.745 Round 3: 377 peptides, 30 chains. Longest chain 32 peptides. Score 0.783 Round 4: 374 peptides, 34 chains. Longest chain 32 peptides. Score 0.754 Round 5: 357 peptides, 34 chains. Longest chain 31 peptides. Score 0.729 Taking the results from Round 3 Chains 31, Residues 347, Estimated correctness of the model 97.4 % 3 chains (72 residues) have been docked in sequence Building loops using Loopy2018 31 chains (347 residues) following loop building 3 chains (72 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 10253 restraints for refining 5441 atoms. 8578 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2477 (Rfree = 0.000) for 5441 atoms. Found 232 (295 requested) and removed 73 (147 requested) atoms. Cycle 32: After refmac, R = 0.2333 (Rfree = 0.000) for 5598 atoms. Found 124 (303 requested) and removed 25 (151 requested) atoms. Cycle 33: After refmac, R = 0.2252 (Rfree = 0.000) for 5688 atoms. Found 109 (309 requested) and removed 20 (154 requested) atoms. Cycle 34: After refmac, R = 0.2187 (Rfree = 0.000) for 5772 atoms. Found 82 (313 requested) and removed 26 (156 requested) atoms. Cycle 35: After refmac, R = 0.2151 (Rfree = 0.000) for 5824 atoms. Found 94 (316 requested) and removed 21 (158 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.00 2.03 NCS extension: 9 residues added (19 deleted due to clashes), 5914 seeds are put forward Round 1: 365 peptides, 38 chains. Longest chain 30 peptides. Score 0.712 Round 2: 370 peptides, 32 chains. Longest chain 33 peptides. Score 0.761 Round 3: 357 peptides, 32 chains. Longest chain 31 peptides. Score 0.743 Round 4: 363 peptides, 33 chains. Longest chain 30 peptides. Score 0.745 Round 5: 373 peptides, 34 chains. Longest chain 33 peptides. Score 0.752 Taking the results from Round 2 Chains 34, Residues 338, Estimated correctness of the model 96.9 % 3 chains (77 residues) have been docked in sequence Building loops using Loopy2018 34 chains (338 residues) following loop building 3 chains (77 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 10811 restraints for refining 5616 atoms. 9145 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2409 (Rfree = 0.000) for 5616 atoms. Found 231 (305 requested) and removed 61 (152 requested) atoms. Cycle 37: After refmac, R = 0.2251 (Rfree = 0.000) for 5780 atoms. Found 135 (313 requested) and removed 23 (156 requested) atoms. Cycle 38: After refmac, R = 0.2182 (Rfree = 0.000) for 5884 atoms. Found 117 (319 requested) and removed 31 (159 requested) atoms. Cycle 39: After refmac, R = 0.2124 (Rfree = 0.000) for 5966 atoms. Found 109 (323 requested) and removed 26 (161 requested) atoms. Cycle 40: After refmac, R = 0.2086 (Rfree = 0.000) for 6047 atoms. Found 101 (328 requested) and removed 50 (164 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.98 2.01 NCS extension: 5 residues added (20 deleted due to clashes), 6108 seeds are put forward Round 1: 351 peptides, 36 chains. Longest chain 27 peptides. Score 0.705 Round 2: 357 peptides, 33 chains. Longest chain 33 peptides. Score 0.736 Round 3: 359 peptides, 33 chains. Longest chain 30 peptides. Score 0.739 Round 4: 354 peptides, 37 chains. Longest chain 31 peptides. Score 0.702 Round 5: 359 peptides, 31 chains. Longest chain 31 peptides. Score 0.753 Taking the results from Round 5 Chains 36, Residues 328, Estimated correctness of the model 96.7 % 5 chains (72 residues) have been docked in sequence Building loops using Loopy2018 36 chains (328 residues) following loop building 5 chains (72 residues) in sequence following loop building ------------------------------------------------------ 59787 reflections ( 99.90 % complete ) and 10913 restraints for refining 5713 atoms. 9339 conditional restraints added. Observations/parameters ratio is 2.62 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2406 (Rfree = 0.000) for 5713 atoms. Found 265 (310 requested) and removed 50 (155 requested) atoms. Cycle 42: After refmac, R = 0.2250 (Rfree = 0.000) for 5924 atoms. Found 145 (321 requested) and removed 15 (160 requested) atoms. Cycle 43: After refmac, R = 0.2151 (Rfree = 0.000) for 6047 atoms. Found 110 (328 requested) and removed 37 (164 requested) atoms. Cycle 44: After refmac, R = 0.2075 (Rfree = 0.000) for 6116 atoms. Found 121 (332 requested) and removed 28 (166 requested) atoms. Cycle 45: After refmac, R = 0.2028 (Rfree = 0.000) for 6202 atoms. Found 91 (337 requested) and removed 40 (168 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.99 2.02 NCS extension: 7 residues added (12 deleted due to clashes), 6269 seeds are put forward Round 1: 343 peptides, 33 chains. Longest chain 31 peptides. Score 0.714 Round 2: 352 peptides, 29 chains. Longest chain 33 peptides. Score 0.757 Round 3: 348 peptides, 33 chains. Longest chain 31 peptides. Score 0.722 Round 4: 357 peptides, 31 chains. Longest chain 31 peptides. Score 0.750 Round 5: 348 peptides, 30 chains. Longest chain 31 peptides. Score 0.744 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 323, Estimated correctness of the model 96.8 % 2 chains (47 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2i5i-1_warpNtrace.pdb as input Building loops using Loopy2018 29 chains (323 residues) following loop building 2 chains (47 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 59787 reflections ( 99.90 % complete ) and 11904 restraints for refining 5908 atoms. 10438 conditional restraints added. Observations/parameters ratio is 2.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2230 (Rfree = 0.000) for 5908 atoms. Found 0 (321 requested) and removed 9 (160 requested) atoms. Cycle 47: After refmac, R = 0.2166 (Rfree = 0.000) for 5897 atoms. Found 0 (314 requested) and removed 5 (160 requested) atoms. Cycle 48: After refmac, R = 0.2139 (Rfree = 0.000) for 5891 atoms. Found 0 (307 requested) and removed 1 (160 requested) atoms. Cycle 49: After refmac, R = 0.2121 (Rfree = 0.000) for 5890 atoms. TimeTaking 72.43