null Mon 24 Dec 07:26:24 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 2pke-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.8-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/2pke-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.8-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 07:26:28 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/2pke-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.8-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 283 and 0 Target number of residues in the AU: 283 Target solvent content: 0.6592 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-3.8-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 4016 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 3 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: 61.213 3.800 Wilson plot Bfac: 84.18 4203 reflections ( 95.76 % complete ) and 0 restraints for refining 4422 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3140 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3094 (Rfree = 0.000) for 4422 atoms. Found 24 (24 requested) and removed 63 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 4500 seeds are put forward NCS extension: 0 residues added, 4500 seeds are put forward Round 1: 105 peptides, 23 chains. Longest chain 7 peptides. Score 0.229 Round 2: 145 peptides, 29 chains. Longest chain 10 peptides. Score 0.292 Round 3: 167 peptides, 32 chains. Longest chain 9 peptides. Score 0.329 Round 4: 170 peptides, 31 chains. Longest chain 9 peptides. Score 0.356 Round 5: 180 peptides, 31 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 5 Chains 31, Residues 149, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 8756 restraints for refining 3631 atoms. 8135 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2646 (Rfree = 0.000) for 3631 atoms. Found 19 (19 requested) and removed 38 (9 requested) atoms. Cycle 2: After refmac, R = 0.2710 (Rfree = 0.000) for 3565 atoms. Found 19 (19 requested) and removed 39 (9 requested) atoms. Cycle 3: After refmac, R = 0.2536 (Rfree = 0.000) for 3496 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 4: After refmac, R = 0.2024 (Rfree = 0.000) for 3455 atoms. Found 14 (19 requested) and removed 21 (9 requested) atoms. Cycle 5: After refmac, R = 0.1936 (Rfree = 0.000) for 3431 atoms. Found 13 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 3610 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3632 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.251 Round 2: 164 peptides, 31 chains. Longest chain 17 peptides. Score 0.333 Round 3: 180 peptides, 32 chains. Longest chain 11 peptides. Score 0.377 Round 4: 164 peptides, 28 chains. Longest chain 14 peptides. Score 0.382 Round 5: 175 peptides, 30 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 5 Chains 30, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7815 restraints for refining 3257 atoms. 7265 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2346 (Rfree = 0.000) for 3257 atoms. Found 17 (17 requested) and removed 36 (8 requested) atoms. Cycle 7: After refmac, R = 0.2331 (Rfree = 0.000) for 3225 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 8: After refmac, R = 0.2435 (Rfree = 0.000) for 3211 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 9: After refmac, R = 0.2495 (Rfree = 0.000) for 3177 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 10: After refmac, R = 0.2327 (Rfree = 0.000) for 3162 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.91 Search for helices and strands: 0 residues in 0 chains, 3338 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 3348 seeds are put forward Round 1: 144 peptides, 28 chains. Longest chain 9 peptides. Score 0.305 Round 2: 180 peptides, 33 chains. Longest chain 9 peptides. Score 0.362 Round 3: 179 peptides, 30 chains. Longest chain 9 peptides. Score 0.405 Round 4: 195 peptides, 35 chains. Longest chain 10 peptides. Score 0.385 Round 5: 189 peptides, 32 chains. Longest chain 12 peptides. Score 0.410 Taking the results from Round 5 Chains 32, Residues 157, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7443 restraints for refining 3259 atoms. 6780 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2368 (Rfree = 0.000) for 3259 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 12: After refmac, R = 0.2207 (Rfree = 0.000) for 3222 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 13: After refmac, R = 0.1846 (Rfree = 0.000) for 3211 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 14: After refmac, R = 0.1827 (Rfree = 0.000) for 3198 atoms. Found 14 (17 requested) and removed 16 (8 requested) atoms. Cycle 15: After refmac, R = 0.1957 (Rfree = 0.000) for 3193 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 3316 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3329 seeds are put forward Round 1: 163 peptides, 33 chains. Longest chain 9 peptides. Score 0.296 Round 2: 170 peptides, 30 chains. Longest chain 11 peptides. Score 0.372 Round 3: 191 peptides, 32 chains. Longest chain 15 peptides. Score 0.417 Round 4: 183 peptides, 31 chains. Longest chain 15 peptides. Score 0.404 Round 5: 186 peptides, 30 chains. Longest chain 15 peptides. Score 0.430 Taking the results from Round 5 Chains 30, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7463 restraints for refining 3241 atoms. 6869 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2226 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 17: After refmac, R = 0.2200 (Rfree = 0.000) for 3210 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 18: After refmac, R = 0.1679 (Rfree = 0.000) for 3195 atoms. Found 9 (17 requested) and removed 17 (8 requested) atoms. Cycle 19: After refmac, R = 0.1800 (Rfree = 0.000) for 3181 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 20: After refmac, R = 0.1612 (Rfree = 0.000) for 3178 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 4.05 Search for helices and strands: 0 residues in 0 chains, 3298 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3315 seeds are put forward Round 1: 168 peptides, 38 chains. Longest chain 8 peptides. Score 0.233 Round 2: 161 peptides, 29 chains. Longest chain 13 peptides. Score 0.355 Round 3: 166 peptides, 30 chains. Longest chain 13 peptides. Score 0.357 Round 4: 159 peptides, 31 chains. Longest chain 10 peptides. Score 0.314 Round 5: 163 peptides, 31 chains. Longest chain 10 peptides. Score 0.330 Taking the results from Round 3 Chains 30, Residues 136, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7467 restraints for refining 3248 atoms. 6930 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1996 (Rfree = 0.000) for 3248 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 22: After refmac, R = 0.2179 (Rfree = 0.000) for 3221 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 23: After refmac, R = 0.2017 (Rfree = 0.000) for 3201 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 24: After refmac, R = 0.2081 (Rfree = 0.000) for 3182 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 25: After refmac, R = 0.1971 (Rfree = 0.000) for 3174 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 4.06 Search for helices and strands: 0 residues in 0 chains, 3327 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3344 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 10 peptides. Score 0.251 Round 2: 133 peptides, 26 chains. Longest chain 9 peptides. Score 0.295 Round 3: 159 peptides, 28 chains. Longest chain 11 peptides. Score 0.363 Round 4: 160 peptides, 27 chains. Longest chain 12 peptides. Score 0.383 Round 5: 158 peptides, 27 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 4 Chains 27, Residues 133, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7311 restraints for refining 3190 atoms. 6789 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1938 (Rfree = 0.000) for 3190 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 27: After refmac, R = 0.2034 (Rfree = 0.000) for 3168 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 28: After refmac, R = 0.2016 (Rfree = 0.000) for 3145 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 29: After refmac, R = 0.2015 (Rfree = 0.000) for 3133 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 30: After refmac, R = 0.1942 (Rfree = 0.000) for 3125 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 3255 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3269 seeds are put forward Round 1: 102 peptides, 23 chains. Longest chain 7 peptides. Score 0.215 Round 2: 132 peptides, 27 chains. Longest chain 8 peptides. Score 0.273 Round 3: 127 peptides, 25 chains. Longest chain 11 peptides. Score 0.288 Round 4: 131 peptides, 24 chains. Longest chain 12 peptides. Score 0.322 Round 5: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.327 Taking the results from Round 5 Chains 26, Residues 115, Estimated correctness of the model 0.0 % 2 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7181 restraints for refining 3114 atoms. 6701 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2102 (Rfree = 0.000) for 3114 atoms. Found 17 (17 requested) and removed 35 (8 requested) atoms. Cycle 32: After refmac, R = 0.2025 (Rfree = 0.000) for 3086 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 33: After refmac, R = 0.1933 (Rfree = 0.000) for 3075 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 34: After refmac, R = 0.1360 (Rfree = 0.000) for 3070 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.1244 (Rfree = 0.000) for 3055 atoms. Found 12 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 4.11 Search for helices and strands: 0 residues in 0 chains, 3200 seeds are put forward NCS extension: 0 residues added, 3200 seeds are put forward Round 1: 109 peptides, 22 chains. Longest chain 11 peptides. Score 0.266 Round 2: 133 peptides, 26 chains. Longest chain 12 peptides. Score 0.295 Round 3: 170 peptides, 31 chains. Longest chain 13 peptides. Score 0.356 Round 4: 162 peptides, 31 chains. Longest chain 14 peptides. Score 0.326 Round 5: 155 peptides, 27 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 5 Chains 28, Residues 128, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7089 restraints for refining 3146 atoms. 6521 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1783 (Rfree = 0.000) for 3146 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 37: After refmac, R = 0.1817 (Rfree = 0.000) for 3109 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 38: After refmac, R = 0.1778 (Rfree = 0.000) for 3102 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 39: After refmac, R = 0.1787 (Rfree = 0.000) for 3099 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 40: After refmac, R = 0.1754 (Rfree = 0.000) for 3097 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 3 residues added (1 deleted due to clashes), 3246 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 11 peptides. Score 0.262 Round 2: 140 peptides, 27 chains. Longest chain 13 peptides. Score 0.306 Round 3: 139 peptides, 25 chains. Longest chain 13 peptides. Score 0.336 Round 4: 141 peptides, 26 chains. Longest chain 13 peptides. Score 0.327 Round 5: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.357 Taking the results from Round 5 Chains 27, Residues 126, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4203 reflections ( 95.76 % complete ) and 7136 restraints for refining 3147 atoms. 6586 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1929 (Rfree = 0.000) for 3147 atoms. Found 17 (17 requested) and removed 38 (8 requested) atoms. Cycle 42: After refmac, R = 0.1803 (Rfree = 0.000) for 3112 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 43: After refmac, R = 0.1923 (Rfree = 0.000) for 3096 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 44: After refmac, R = 0.1653 (Rfree = 0.000) for 3082 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.1222 (Rfree = 0.000) for 3079 atoms. Found 10 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 3237 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3246 seeds are put forward Round 1: 94 peptides, 20 chains. Longest chain 10 peptides. Score 0.236 Round 2: 115 peptides, 22 chains. Longest chain 11 peptides. Score 0.291 Round 3: 121 peptides, 22 chains. Longest chain 13 peptides. Score 0.317 Round 4: 121 peptides, 22 chains. Longest chain 13 peptides. Score 0.317 Round 5: 114 peptides, 21 chains. Longest chain 13 peptides. Score 0.306 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 99, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence Sequence coverage is 38 % Consider running further cycles of model building using 2pke-3_warpNtrace.pdb as input Building loops using Loopy2018 22 chains (99 residues) following loop building 6 chains (38 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4203 reflections ( 95.76 % complete ) and 6968 restraints for refining 3110 atoms. 6473 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1803 (Rfree = 0.000) for 3110 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2001 (Rfree = 0.000) for 3090 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1928 (Rfree = 0.000) for 3072 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1404 (Rfree = 0.000) for 3060 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:00:28 GMT 2018 Job finished. TimeTaking 34.07 Used memory is bytes: 2066360