null Sun 23 Dec 22:22:56 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 2opk-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2opk-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2opk-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-2.1-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/2opk-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-2.1-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 ============================================================ Sun 23 Dec 22:23:05 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/2opk-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2opk-2.1-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 592 and 0 Target number of residues in the AU: 592 Target solvent content: 0.4361 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-2.1-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.60 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: 28.177 2.101 Wilson plot Bfac: 12.57 34444 reflections ( 99.66 % complete ) and 0 restraints for refining 4000 atoms. Observations/parameters ratio is 2.15 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2730 (Rfree = 0.000) for 4000 atoms. Found 119 (119 requested) and removed 61 (59 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.97 1.79 NCS extension: 0 residues added, 4058 seeds are put forward Round 1: 343 peptides, 37 chains. Longest chain 40 peptides. Score 0.680 Round 2: 394 peptides, 24 chains. Longest chain 51 peptides. Score 0.833 Round 3: 408 peptides, 14 chains. Longest chain 75 peptides. Score 0.891 Round 4: 411 peptides, 15 chains. Longest chain 100 peptides. Score 0.888 Round 5: 423 peptides, 10 chains. Longest chain 109 peptides. Score 0.915 Taking the results from Round 5 Chains 13, Residues 413, Estimated correctness of the model 99.1 % 8 chains (397 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 31 A Built loop between residues 66 C and 72 C Built loop between residues 72 D and 79 D Built loop between residues 89 D and 93 D 7 chains (425 residues) following loop building 4 chains (414 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 3956 restraints for refining 3917 atoms. 581 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2938 (Rfree = 0.000) for 3917 atoms. Found 116 (116 requested) and removed 58 (58 requested) atoms. Cycle 2: After refmac, R = 0.2784 (Rfree = 0.000) for 3968 atoms. Found 92 (118 requested) and removed 22 (59 requested) atoms. Cycle 3: After refmac, R = 0.2615 (Rfree = 0.000) for 4023 atoms. Found 93 (120 requested) and removed 23 (60 requested) atoms. Cycle 4: After refmac, R = 0.2502 (Rfree = 0.000) for 4080 atoms. Found 67 (121 requested) and removed 12 (60 requested) atoms. Cycle 5: After refmac, R = 0.2423 (Rfree = 0.000) for 4122 atoms. Found 69 (123 requested) and removed 17 (61 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.82 1.66 NCS extension: 9 residues added (86 deleted due to clashes), 4190 seeds are put forward Round 1: 424 peptides, 8 chains. Longest chain 97 peptides. Score 0.922 Round 2: 427 peptides, 7 chains. Longest chain 109 peptides. Score 0.927 Round 3: 419 peptides, 10 chains. Longest chain 66 peptides. Score 0.913 Round 4: 422 peptides, 10 chains. Longest chain 108 peptides. Score 0.914 Round 5: 421 peptides, 12 chains. Longest chain 96 peptides. Score 0.906 Taking the results from Round 2 Chains 9, Residues 420, Estimated correctness of the model 99.3 % 7 chains (417 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 31 A Built loop between residues 52 C and 55 C Built loop between residues 68 D and 73 D 4 chains (426 residues) following loop building 4 chains (426 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 3949 restraints for refining 3999 atoms. 524 conditional restraints added. Observations/parameters ratio is 2.15 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2459 (Rfree = 0.000) for 3999 atoms. Found 119 (119 requested) and removed 40 (59 requested) atoms. Cycle 7: After refmac, R = 0.2358 (Rfree = 0.000) for 4070 atoms. Found 83 (121 requested) and removed 27 (60 requested) atoms. Cycle 8: After refmac, R = 0.2284 (Rfree = 0.000) for 4122 atoms. Found 70 (122 requested) and removed 27 (61 requested) atoms. Cycle 9: After refmac, R = 0.2229 (Rfree = 0.000) for 4161 atoms. Found 72 (123 requested) and removed 29 (61 requested) atoms. Cycle 10: After refmac, R = 0.2209 (Rfree = 0.000) for 4196 atoms. Found 67 (125 requested) and removed 35 (62 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.81 1.65 NCS extension: 0 residues added, 4231 seeds are put forward Round 1: 425 peptides, 7 chains. Longest chain 106 peptides. Score 0.926 Round 2: 423 peptides, 6 chains. Longest chain 109 peptides. Score 0.929 Round 3: 426 peptides, 9 chains. Longest chain 109 peptides. Score 0.920 Round 4: 428 peptides, 6 chains. Longest chain 109 peptides. Score 0.931 Round 5: 421 peptides, 9 chains. Longest chain 96 peptides. Score 0.917 Taking the results from Round 4 Chains 7, Residues 422, Estimated correctness of the model 99.4 % 6 chains (421 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 C and 18 C Built loop between residues 44 B and 47 B 5 chains (426 residues) following loop building 4 chains (425 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 3996 restraints for refining 4030 atoms. 577 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2320 (Rfree = 0.000) for 4030 atoms. Found 117 (117 requested) and removed 39 (59 requested) atoms. Cycle 12: After refmac, R = 0.2242 (Rfree = 0.000) for 4105 atoms. Found 90 (120 requested) and removed 15 (61 requested) atoms. Cycle 13: After refmac, R = 0.2195 (Rfree = 0.000) for 4179 atoms. Found 85 (122 requested) and removed 25 (62 requested) atoms. Cycle 14: After refmac, R = 0.2178 (Rfree = 0.000) for 4233 atoms. Found 77 (123 requested) and removed 32 (63 requested) atoms. Cycle 15: After refmac, R = 0.2170 (Rfree = 0.000) for 4273 atoms. Found 78 (124 requested) and removed 38 (63 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.78 1.62 NCS extension: 0 residues added, 4314 seeds are put forward Round 1: 423 peptides, 5 chains. Longest chain 108 peptides. Score 0.932 Round 2: 422 peptides, 7 chains. Longest chain 103 peptides. Score 0.925 Round 3: 424 peptides, 10 chains. Longest chain 108 peptides. Score 0.915 Round 4: 420 peptides, 8 chains. Longest chain 109 peptides. Score 0.920 Round 5: 426 peptides, 6 chains. Longest chain 109 peptides. Score 0.930 Taking the results from Round 1 Chains 5, Residues 418, Estimated correctness of the model 99.4 % 5 chains (418 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 D and 74 D 4 chains (423 residues) following loop building 4 chains (423 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4054 restraints for refining 4112 atoms. 649 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2259 (Rfree = 0.000) for 4112 atoms. Found 120 (120 requested) and removed 25 (61 requested) atoms. Cycle 17: After refmac, R = 0.2199 (Rfree = 0.000) for 4203 atoms. Found 85 (122 requested) and removed 22 (62 requested) atoms. Cycle 18: After refmac, R = 0.2155 (Rfree = 0.000) for 4264 atoms. Found 80 (123 requested) and removed 30 (63 requested) atoms. Cycle 19: After refmac, R = 0.2128 (Rfree = 0.000) for 4309 atoms. Found 96 (125 requested) and removed 33 (64 requested) atoms. Cycle 20: After refmac, R = 0.2109 (Rfree = 0.000) for 4366 atoms. Found 81 (127 requested) and removed 48 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.77 1.61 NCS extension: 0 residues added, 4399 seeds are put forward Round 1: 425 peptides, 8 chains. Longest chain 107 peptides. Score 0.923 Round 2: 426 peptides, 5 chains. Longest chain 108 peptides. Score 0.933 Round 3: 429 peptides, 5 chains. Longest chain 109 peptides. Score 0.935 Round 4: 424 peptides, 11 chains. Longest chain 66 peptides. Score 0.912 Round 5: 427 peptides, 8 chains. Longest chain 107 peptides. Score 0.924 Taking the results from Round 3 Chains 5, Residues 424, Estimated correctness of the model 99.4 % 5 chains (424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 C and 46 C 4 chains (426 residues) following loop building 4 chains (426 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4065 restraints for refining 4167 atoms. 635 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2211 (Rfree = 0.000) for 4167 atoms. Found 119 (119 requested) and removed 34 (62 requested) atoms. Cycle 22: After refmac, R = 0.2145 (Rfree = 0.000) for 4240 atoms. Found 105 (121 requested) and removed 25 (63 requested) atoms. Cycle 23: After refmac, R = 0.2122 (Rfree = 0.000) for 4315 atoms. Found 81 (123 requested) and removed 42 (64 requested) atoms. Cycle 24: After refmac, R = 0.2104 (Rfree = 0.000) for 4348 atoms. Found 97 (121 requested) and removed 40 (64 requested) atoms. Cycle 25: After refmac, R = 0.2100 (Rfree = 0.000) for 4402 atoms. Found 67 (123 requested) and removed 66 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.77 1.61 NCS extension: 0 residues added, 4403 seeds are put forward Round 1: 426 peptides, 7 chains. Longest chain 107 peptides. Score 0.927 Round 2: 427 peptides, 5 chains. Longest chain 108 peptides. Score 0.934 Round 3: 428 peptides, 6 chains. Longest chain 109 peptides. Score 0.931 Round 4: 424 peptides, 10 chains. Longest chain 107 peptides. Score 0.915 Round 5: 426 peptides, 8 chains. Longest chain 105 peptides. Score 0.923 Taking the results from Round 2 Chains 5, Residues 422, Estimated correctness of the model 99.4 % 5 chains (422 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A 4 chains (424 residues) following loop building 4 chains (424 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4113 restraints for refining 4183 atoms. 703 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2207 (Rfree = 0.000) for 4183 atoms. Found 114 (114 requested) and removed 38 (62 requested) atoms. Cycle 27: After refmac, R = 0.2146 (Rfree = 0.000) for 4248 atoms. Found 115 (116 requested) and removed 23 (63 requested) atoms. Cycle 28: After refmac, R = 0.2115 (Rfree = 0.000) for 4336 atoms. Found 104 (119 requested) and removed 39 (64 requested) atoms. Cycle 29: After refmac, R = 0.2093 (Rfree = 0.000) for 4398 atoms. Found 88 (120 requested) and removed 41 (65 requested) atoms. Cycle 30: After refmac, R = 0.2080 (Rfree = 0.000) for 4439 atoms. Found 96 (121 requested) and removed 36 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.76 1.60 NCS extension: 0 residues added, 4499 seeds are put forward Round 1: 426 peptides, 5 chains. Longest chain 108 peptides. Score 0.933 Round 2: 426 peptides, 5 chains. Longest chain 109 peptides. Score 0.933 Round 3: 426 peptides, 9 chains. Longest chain 109 peptides. Score 0.920 Round 4: 427 peptides, 9 chains. Longest chain 93 peptides. Score 0.920 Round 5: 426 peptides, 9 chains. Longest chain 99 peptides. Score 0.920 Taking the results from Round 2 Chains 5, Residues 421, Estimated correctness of the model 99.4 % 5 chains (421 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 74 A 4 chains (425 residues) following loop building 4 chains (425 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4191 restraints for refining 4252 atoms. 773 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2183 (Rfree = 0.000) for 4252 atoms. Found 116 (116 requested) and removed 29 (63 requested) atoms. Cycle 32: After refmac, R = 0.2137 (Rfree = 0.000) for 4331 atoms. Found 112 (119 requested) and removed 20 (64 requested) atoms. Cycle 33: After refmac, R = 0.2090 (Rfree = 0.000) for 4420 atoms. Found 80 (121 requested) and removed 25 (65 requested) atoms. Cycle 34: After refmac, R = 0.2067 (Rfree = 0.000) for 4470 atoms. Found 64 (122 requested) and removed 36 (66 requested) atoms. Cycle 35: After refmac, R = 0.2058 (Rfree = 0.000) for 4490 atoms. Found 75 (120 requested) and removed 32 (66 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.76 1.60 NCS extension: 3 residues added (0 deleted due to clashes), 4536 seeds are put forward Round 1: 428 peptides, 6 chains. Longest chain 110 peptides. Score 0.931 Round 2: 433 peptides, 5 chains. Longest chain 110 peptides. Score 0.936 Round 3: 429 peptides, 8 chains. Longest chain 106 peptides. Score 0.925 Round 4: 430 peptides, 8 chains. Longest chain 110 peptides. Score 0.925 Round 5: 430 peptides, 8 chains. Longest chain 110 peptides. Score 0.925 Taking the results from Round 2 Chains 5, Residues 428, Estimated correctness of the model 99.5 % 5 chains (428 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A 4 chains (430 residues) following loop building 4 chains (430 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4231 restraints for refining 4302 atoms. 777 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2176 (Rfree = 0.000) for 4302 atoms. Found 115 (115 requested) and removed 35 (64 requested) atoms. Cycle 37: After refmac, R = 0.2123 (Rfree = 0.000) for 4377 atoms. Found 105 (117 requested) and removed 29 (65 requested) atoms. Cycle 38: After refmac, R = 0.2084 (Rfree = 0.000) for 4451 atoms. Found 96 (119 requested) and removed 32 (66 requested) atoms. Cycle 39: After refmac, R = 0.2068 (Rfree = 0.000) for 4513 atoms. Found 77 (121 requested) and removed 43 (67 requested) atoms. Cycle 40: After refmac, R = 0.2054 (Rfree = 0.000) for 4542 atoms. Found 87 (119 requested) and removed 51 (67 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.75 1.59 NCS extension: 0 residues added, 4579 seeds are put forward Round 1: 429 peptides, 6 chains. Longest chain 110 peptides. Score 0.931 Round 2: 430 peptides, 7 chains. Longest chain 110 peptides. Score 0.929 Round 3: 426 peptides, 8 chains. Longest chain 106 peptides. Score 0.923 Round 4: 422 peptides, 11 chains. Longest chain 75 peptides. Score 0.911 Round 5: 424 peptides, 7 chains. Longest chain 106 peptides. Score 0.926 Taking the results from Round 1 Chains 6, Residues 423, Estimated correctness of the model 99.4 % 6 chains (423 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 C and 31 C Built loop between residues 69 D and 72 D 4 chains (428 residues) following loop building 4 chains (428 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4253 restraints for refining 4344 atoms. 812 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2152 (Rfree = 0.000) for 4344 atoms. Found 111 (111 requested) and removed 30 (64 requested) atoms. Cycle 42: After refmac, R = 0.2101 (Rfree = 0.000) for 4416 atoms. Found 113 (113 requested) and removed 30 (65 requested) atoms. Cycle 43: After refmac, R = 0.2090 (Rfree = 0.000) for 4495 atoms. Found 100 (114 requested) and removed 40 (66 requested) atoms. Cycle 44: After refmac, R = 0.2064 (Rfree = 0.000) for 4549 atoms. Found 92 (116 requested) and removed 41 (67 requested) atoms. Cycle 45: After refmac, R = 0.2066 (Rfree = 0.000) for 4594 atoms. Found 85 (117 requested) and removed 60 (68 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.77 1.61 NCS extension: 5 residues added (78 deleted due to clashes), 4626 seeds are put forward Round 1: 419 peptides, 6 chains. Longest chain 106 peptides. Score 0.927 Round 2: 425 peptides, 5 chains. Longest chain 107 peptides. Score 0.933 Round 3: 424 peptides, 9 chains. Longest chain 106 peptides. Score 0.919 Round 4: 421 peptides, 7 chains. Longest chain 110 peptides. Score 0.924 Round 5: 423 peptides, 7 chains. Longest chain 110 peptides. Score 0.925 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 420, Estimated correctness of the model 99.4 % 5 chains (420 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 68 A and 72 A 4 chains (423 residues) following loop building 4 chains (423 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 34444 reflections ( 99.66 % complete ) and 3399 restraints for refining 3286 atoms. Observations/parameters ratio is 2.62 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2709 (Rfree = 0.000) for 3286 atoms. Found 48 (81 requested) and removed 0 (81 requested) atoms. Cycle 47: After refmac, R = 0.2546 (Rfree = 0.000) for 3286 atoms. Found 17 (83 requested) and removed 0 (49 requested) atoms. Cycle 48: After refmac, R = 0.2479 (Rfree = 0.000) for 3286 atoms. Found 11 (83 requested) and removed 3 (49 requested) atoms. Cycle 49: After refmac, R = 0.2444 (Rfree = 0.000) for 3286 atoms. Found 7 (83 requested) and removed 3 (49 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:35:35 GMT 2018 Job finished. TimeTaking 72.66 Used memory is bytes: 15466856