Mon 24 Dec 07:26:56 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 2opl-1.5-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opl-1.5-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opl-1.5-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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/2opl-1.5-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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 07:27:01 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/2opl-1.5-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opl-1.5-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 406 and 0 Target number of residues in the AU: 406 Target solvent content: 0.4115 Checking the provided sequence file Detected sequence length: 187 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 374 Adjusted target solvent content: 0.46 Input MTZ file: 2opl-1.5-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: 19 Cell parameters: 47.200 82.950 95.370 90.000 90.000 90.000 Input sequence file: 2opl-1.5-parrot-noncs.fasta_lf Building free atoms model in initial map for 2992 target number of atoms Had to go as low as 0.35 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: 62.588 1.500 Wilson plot Bfac: 9.25 60683 reflections ( 99.87 % complete ) and 0 restraints for refining 3297 atoms. Observations/parameters ratio is 4.60 ------------------------------------------------------ Starting model: R = 0.3351 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2821 (Rfree = 0.000) for 3297 atoms. Found 256 (256 requested) and removed 145 (128 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.41 1.49 NCS extension: 0 residues added, 3408 seeds are put forward Round 1: 319 peptides, 17 chains. Longest chain 50 peptides. Score 0.894 Round 2: 339 peptides, 10 chains. Longest chain 78 peptides. Score 0.939 Round 3: 342 peptides, 8 chains. Longest chain 111 peptides. Score 0.948 Round 4: 351 peptides, 7 chains. Longest chain 109 peptides. Score 0.955 Round 5: 352 peptides, 6 chains. Longest chain 127 peptides. Score 0.959 Taking the results from Round 5 Chains 6, Residues 346, Estimated correctness of the model 99.9 % 6 chains (346 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 23 A Built loop between residues 54 A and 57 A Built loop between residues 70 A and 74 A Built loop between residues 131 B and 136 B 2 chains (358 residues) following loop building 2 chains (358 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3100 restraints for refining 3215 atoms. 285 conditional restraints added. Observations/parameters ratio is 4.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2620 (Rfree = 0.000) for 3215 atoms. Found 159 (250 requested) and removed 66 (125 requested) atoms. Cycle 2: After refmac, R = 0.2374 (Rfree = 0.000) for 3306 atoms. Found 127 (257 requested) and removed 19 (128 requested) atoms. Cycle 3: After refmac, R = 0.2227 (Rfree = 0.000) for 3410 atoms. Found 96 (265 requested) and removed 20 (132 requested) atoms. Cycle 4: After refmac, R = 0.2013 (Rfree = 0.000) for 3485 atoms. Found 102 (271 requested) and removed 26 (135 requested) atoms. Cycle 5: After refmac, R = 0.1899 (Rfree = 0.000) for 3553 atoms. Found 108 (276 requested) and removed 27 (138 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.37 1.45 NCS extension: 5 residues added (175 deleted due to clashes), 3641 seeds are put forward Round 1: 356 peptides, 4 chains. Longest chain 136 peptides. Score 0.967 Round 2: 352 peptides, 3 chains. Longest chain 180 peptides. Score 0.968 Round 3: 352 peptides, 5 chains. Longest chain 125 peptides. Score 0.962 Round 4: 353 peptides, 5 chains. Longest chain 180 peptides. Score 0.963 Round 5: 352 peptides, 5 chains. Longest chain 98 peptides. Score 0.962 Taking the results from Round 2 Chains 3, Residues 349, Estimated correctness of the model 99.9 % 3 chains (349 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 139 A 2 chains (356 residues) following loop building 2 chains (356 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3261 restraints for refining 3444 atoms. 456 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2227 (Rfree = 0.000) for 3444 atoms. Found 143 (267 requested) and removed 51 (133 requested) atoms. Cycle 7: After refmac, R = 0.1972 (Rfree = 0.000) for 3533 atoms. Found 117 (275 requested) and removed 28 (137 requested) atoms. Cycle 8: After refmac, R = 0.1864 (Rfree = 0.000) for 3615 atoms. Found 114 (281 requested) and removed 40 (140 requested) atoms. Cycle 9: After refmac, R = 0.1817 (Rfree = 0.000) for 3681 atoms. Found 98 (286 requested) and removed 53 (143 requested) atoms. Cycle 10: After refmac, R = 0.1779 (Rfree = 0.000) for 3723 atoms. Found 115 (283 requested) and removed 45 (144 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.37 1.45 NCS extension: 4 residues added (178 deleted due to clashes), 3799 seeds are put forward Round 1: 355 peptides, 4 chains. Longest chain 136 peptides. Score 0.966 Round 2: 352 peptides, 3 chains. Longest chain 180 peptides. Score 0.968 Round 3: 352 peptides, 6 chains. Longest chain 165 peptides. Score 0.959 Round 4: 354 peptides, 4 chains. Longest chain 136 peptides. Score 0.966 Round 5: 351 peptides, 5 chains. Longest chain 165 peptides. Score 0.962 Taking the results from Round 2 Chains 3, Residues 349, Estimated correctness of the model 99.9 % 3 chains (349 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 139 A 2 chains (356 residues) following loop building 2 chains (356 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3344 restraints for refining 3513 atoms. 539 conditional restraints added. Observations/parameters ratio is 4.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2160 (Rfree = 0.000) for 3513 atoms. Found 145 (268 requested) and removed 49 (136 requested) atoms. Cycle 12: After refmac, R = 0.1926 (Rfree = 0.000) for 3607 atoms. Found 119 (274 requested) and removed 45 (140 requested) atoms. Cycle 13: After refmac, R = 0.1843 (Rfree = 0.000) for 3673 atoms. Found 107 (280 requested) and removed 40 (143 requested) atoms. Cycle 14: After refmac, R = 0.1798 (Rfree = 0.000) for 3734 atoms. Found 98 (284 requested) and removed 41 (145 requested) atoms. Cycle 15: After refmac, R = 0.1769 (Rfree = 0.000) for 3784 atoms. Found 91 (288 requested) and removed 38 (147 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.36 1.43 NCS extension: 2 residues added (178 deleted due to clashes), 3840 seeds are put forward Round 1: 356 peptides, 4 chains. Longest chain 137 peptides. Score 0.967 Round 2: 353 peptides, 3 chains. Longest chain 180 peptides. Score 0.969 Round 3: 351 peptides, 7 chains. Longest chain 136 peptides. Score 0.955 Round 4: 356 peptides, 3 chains. Longest chain 180 peptides. Score 0.970 Round 5: 355 peptides, 4 chains. Longest chain 180 peptides. Score 0.966 Taking the results from Round 4 Chains 3, Residues 353, Estimated correctness of the model 100.0 % 3 chains (353 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 2 chains (357 residues) following loop building 2 chains (357 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3379 restraints for refining 3541 atoms. 567 conditional restraints added. Observations/parameters ratio is 4.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2163 (Rfree = 0.000) for 3541 atoms. Found 160 (269 requested) and removed 48 (137 requested) atoms. Cycle 17: After refmac, R = 0.1924 (Rfree = 0.000) for 3648 atoms. Found 114 (278 requested) and removed 33 (142 requested) atoms. Cycle 18: After refmac, R = 0.1825 (Rfree = 0.000) for 3723 atoms. Found 101 (284 requested) and removed 25 (145 requested) atoms. Cycle 19: After refmac, R = 0.1778 (Rfree = 0.000) for 3790 atoms. Found 79 (289 requested) and removed 37 (147 requested) atoms. Cycle 20: After refmac, R = 0.1748 (Rfree = 0.000) for 3823 atoms. Found 95 (292 requested) and removed 37 (149 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.37 1.45 NCS extension: 0 residues added, 3881 seeds are put forward Round 1: 355 peptides, 4 chains. Longest chain 136 peptides. Score 0.966 Round 2: 348 peptides, 5 chains. Longest chain 180 peptides. Score 0.961 Round 3: 355 peptides, 4 chains. Longest chain 165 peptides. Score 0.966 Round 4: 354 peptides, 5 chains. Longest chain 136 peptides. Score 0.963 Round 5: 351 peptides, 5 chains. Longest chain 180 peptides. Score 0.962 Taking the results from Round 3 Chains 4, Residues 351, Estimated correctness of the model 99.9 % 3 chains (338 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 3 chains (355 residues) following loop building 2 chains (342 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3536 restraints for refining 3565 atoms. 785 conditional restraints added. Observations/parameters ratio is 4.26 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2157 (Rfree = 0.000) for 3565 atoms. Found 159 (271 requested) and removed 40 (138 requested) atoms. Cycle 22: After refmac, R = 0.1917 (Rfree = 0.000) for 3678 atoms. Found 107 (280 requested) and removed 25 (143 requested) atoms. Cycle 23: After refmac, R = 0.1828 (Rfree = 0.000) for 3752 atoms. Found 89 (286 requested) and removed 27 (146 requested) atoms. Cycle 24: After refmac, R = 0.1787 (Rfree = 0.000) for 3808 atoms. Found 97 (290 requested) and removed 42 (148 requested) atoms. Cycle 25: After refmac, R = 0.1771 (Rfree = 0.000) for 3854 atoms. Found 97 (294 requested) and removed 38 (150 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.38 1.46 NCS extension: 0 residues added (16 deleted due to clashes), 3913 seeds are put forward Round 1: 358 peptides, 4 chains. Longest chain 137 peptides. Score 0.967 Round 2: 360 peptides, 3 chains. Longest chain 181 peptides. Score 0.971 Round 3: 357 peptides, 5 chains. Longest chain 136 peptides. Score 0.964 Round 4: 357 peptides, 5 chains. Longest chain 165 peptides. Score 0.964 Round 5: 357 peptides, 6 chains. Longest chain 136 peptides. Score 0.961 Taking the results from Round 2 Chains 3, Residues 357, Estimated correctness of the model 100.0 % 3 chains (357 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 2 chains (359 residues) following loop building 2 chains (359 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3482 restraints for refining 3609 atoms. 656 conditional restraints added. Observations/parameters ratio is 4.20 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2172 (Rfree = 0.000) for 3609 atoms. Found 171 (274 requested) and removed 42 (140 requested) atoms. Cycle 27: After refmac, R = 0.1920 (Rfree = 0.000) for 3736 atoms. Found 98 (284 requested) and removed 36 (145 requested) atoms. Cycle 28: After refmac, R = 0.1825 (Rfree = 0.000) for 3787 atoms. Found 96 (289 requested) and removed 31 (147 requested) atoms. Cycle 29: After refmac, R = 0.1773 (Rfree = 0.000) for 3842 atoms. Found 98 (293 requested) and removed 27 (149 requested) atoms. Cycle 30: After refmac, R = 0.1755 (Rfree = 0.000) for 3907 atoms. Found 78 (298 requested) and removed 42 (152 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.37 1.45 NCS extension: 0 residues added, 3943 seeds are put forward Round 1: 356 peptides, 4 chains. Longest chain 136 peptides. Score 0.967 Round 2: 354 peptides, 6 chains. Longest chain 128 peptides. Score 0.960 Round 3: 353 peptides, 4 chains. Longest chain 136 peptides. Score 0.966 Round 4: 357 peptides, 4 chains. Longest chain 165 peptides. Score 0.967 Round 5: 354 peptides, 6 chains. Longest chain 128 peptides. Score 0.960 Taking the results from Round 4 Chains 5, Residues 353, Estimated correctness of the model 99.9 % 3 chains (336 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 135 A 4 chains (356 residues) following loop building 2 chains (339 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3713 restraints for refining 3631 atoms. 971 conditional restraints added. Observations/parameters ratio is 4.18 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2164 (Rfree = 0.000) for 3631 atoms. Found 168 (271 requested) and removed 44 (141 requested) atoms. Cycle 32: After refmac, R = 0.1938 (Rfree = 0.000) for 3753 atoms. Found 106 (280 requested) and removed 31 (146 requested) atoms. Cycle 33: After refmac, R = 0.1833 (Rfree = 0.000) for 3819 atoms. Found 88 (285 requested) and removed 32 (148 requested) atoms. Cycle 34: After refmac, R = 0.1785 (Rfree = 0.000) for 3870 atoms. Found 98 (289 requested) and removed 42 (150 requested) atoms. Cycle 35: After refmac, R = 0.1759 (Rfree = 0.000) for 3917 atoms. Found 104 (293 requested) and removed 54 (152 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.37 1.45 NCS extension: 1 residues added (20 deleted due to clashes), 3968 seeds are put forward Round 1: 354 peptides, 5 chains. Longest chain 136 peptides. Score 0.963 Round 2: 349 peptides, 6 chains. Longest chain 163 peptides. Score 0.958 Round 3: 354 peptides, 4 chains. Longest chain 163 peptides. Score 0.966 Round 4: 351 peptides, 4 chains. Longest chain 136 peptides. Score 0.965 Round 5: 344 peptides, 7 chains. Longest chain 164 peptides. Score 0.952 Taking the results from Round 3 Chains 4, Residues 350, Estimated correctness of the model 99.9 % 3 chains (335 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 136 A 3 chains (354 residues) following loop building 2 chains (339 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3715 restraints for refining 3632 atoms. 980 conditional restraints added. Observations/parameters ratio is 4.18 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2169 (Rfree = 0.000) for 3632 atoms. Found 181 (265 requested) and removed 47 (141 requested) atoms. Cycle 37: After refmac, R = 0.1941 (Rfree = 0.000) for 3762 atoms. Found 121 (274 requested) and removed 28 (146 requested) atoms. Cycle 38: After refmac, R = 0.1840 (Rfree = 0.000) for 3848 atoms. Found 88 (281 requested) and removed 27 (149 requested) atoms. Cycle 39: After refmac, R = 0.1779 (Rfree = 0.000) for 3901 atoms. Found 83 (286 requested) and removed 26 (152 requested) atoms. Cycle 40: After refmac, R = 0.1757 (Rfree = 0.000) for 3952 atoms. Found 76 (289 requested) and removed 43 (153 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.37 1.45 NCS extension: 0 residues added (17 deleted due to clashes), 3985 seeds are put forward Round 1: 351 peptides, 4 chains. Longest chain 136 peptides. Score 0.965 Round 2: 350 peptides, 4 chains. Longest chain 171 peptides. Score 0.965 Round 3: 350 peptides, 8 chains. Longest chain 136 peptides. Score 0.951 Round 4: 349 peptides, 5 chains. Longest chain 163 peptides. Score 0.961 Round 5: 353 peptides, 6 chains. Longest chain 136 peptides. Score 0.959 Taking the results from Round 2 Chains 4, Residues 346, Estimated correctness of the model 99.9 % 3 chains (340 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 136 A 3 chains (353 residues) following loop building 2 chains (347 residues) in sequence following loop building ------------------------------------------------------ 60683 reflections ( 99.87 % complete ) and 3779 restraints for refining 3685 atoms. 1017 conditional restraints added. Observations/parameters ratio is 4.12 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2168 (Rfree = 0.000) for 3685 atoms. Found 182 (263 requested) and removed 42 (143 requested) atoms. Cycle 42: After refmac, R = 0.1949 (Rfree = 0.000) for 3822 atoms. Found 105 (273 requested) and removed 34 (148 requested) atoms. Cycle 43: After refmac, R = 0.1847 (Rfree = 0.000) for 3878 atoms. Found 107 (278 requested) and removed 22 (151 requested) atoms. Cycle 44: After refmac, R = 0.1807 (Rfree = 0.000) for 3953 atoms. Found 88 (283 requested) and removed 42 (154 requested) atoms. Cycle 45: After refmac, R = 0.1768 (Rfree = 0.000) for 3991 atoms. Found 92 (286 requested) and removed 29 (155 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.37 1.45 NCS extension: 3 residues added (177 deleted due to clashes), 4058 seeds are put forward Round 1: 351 peptides, 4 chains. Longest chain 136 peptides. Score 0.965 Round 2: 353 peptides, 3 chains. Longest chain 181 peptides. Score 0.969 Round 3: 349 peptides, 5 chains. Longest chain 144 peptides. Score 0.961 Round 4: 349 peptides, 6 chains. Longest chain 114 peptides. Score 0.958 Round 5: 350 peptides, 5 chains. Longest chain 171 peptides. Score 0.961 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 350, Estimated correctness of the model 100.0 % 3 chains (350 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 128 A and 136 A 2 chains (357 residues) following loop building 2 chains (357 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 60683 reflections ( 99.87 % complete ) and 2812 restraints for refining 2762 atoms. Observations/parameters ratio is 5.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2803 (Rfree = 0.000) for 2762 atoms. Found 159 (197 requested) and removed 0 (197 requested) atoms. Cycle 47: After refmac, R = 0.2274 (Rfree = 0.000) for 2762 atoms. Found 92 (209 requested) and removed 0 (113 requested) atoms. Cycle 48: After refmac, R = 0.2075 (Rfree = 0.000) for 2762 atoms. Found 51 (215 requested) and removed 4 (117 requested) atoms. Cycle 49: After refmac, R = 0.1963 (Rfree = 0.000) for 2762 atoms. TimeTaking 62.83