Mon 24 Dec 07:26:23 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-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pke-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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 307 and 0 Target number of residues in the AU: 307 Target solvent content: 0.6303 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-3.2-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-3.2-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 3.200 Wilson plot Bfac: 66.17 7099 reflections ( 96.62 % complete ) and 0 restraints for refining 4471 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2995 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3039 (Rfree = 0.000) for 4471 atoms. Found 40 (40 requested) and removed 105 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.64 Search for helices and strands: 0 residues in 0 chains, 4511 seeds are put forward NCS extension: 0 residues added, 4511 seeds are put forward Round 1: 137 peptides, 30 chains. Longest chain 9 peptides. Score 0.241 Round 2: 167 peptides, 34 chains. Longest chain 10 peptides. Score 0.296 Round 3: 177 peptides, 33 chains. Longest chain 13 peptides. Score 0.350 Round 4: 188 peptides, 35 chains. Longest chain 14 peptides. Score 0.360 Round 5: 214 peptides, 40 chains. Longest chain 15 peptides. Score 0.377 Taking the results from Round 5 Chains 40, Residues 174, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8778 restraints for refining 3666 atoms. 8101 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2455 (Rfree = 0.000) for 3666 atoms. Found 32 (32 requested) and removed 69 (16 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 3587 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 3: After refmac, R = 0.2134 (Rfree = 0.000) for 3560 atoms. Found 12 (32 requested) and removed 22 (16 requested) atoms. Cycle 4: After refmac, R = 0.2060 (Rfree = 0.000) for 3540 atoms. Found 17 (31 requested) and removed 22 (15 requested) atoms. Cycle 5: After refmac, R = 0.1993 (Rfree = 0.000) for 3526 atoms. Found 10 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.57 Search for helices and strands: 0 residues in 0 chains, 3689 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3709 seeds are put forward Round 1: 186 peptides, 42 chains. Longest chain 9 peptides. Score 0.240 Round 2: 226 peptides, 46 chains. Longest chain 9 peptides. Score 0.330 Round 3: 230 peptides, 44 chains. Longest chain 10 peptides. Score 0.374 Round 4: 220 peptides, 43 chains. Longest chain 12 peptides. Score 0.353 Round 5: 225 peptides, 39 chains. Longest chain 15 peptides. Score 0.430 Taking the results from Round 5 Chains 39, Residues 186, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8112 restraints for refining 3463 atoms. 7391 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2265 (Rfree = 0.000) for 3463 atoms. Found 28 (31 requested) and removed 26 (15 requested) atoms. Cycle 7: After refmac, R = 0.2191 (Rfree = 0.000) for 3453 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 8: After refmac, R = 0.2100 (Rfree = 0.000) for 3450 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 9: After refmac, R = 0.1881 (Rfree = 0.000) for 3450 atoms. Found 9 (31 requested) and removed 23 (15 requested) atoms. Cycle 10: After refmac, R = 0.2594 (Rfree = 0.000) for 3431 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.55 Search for helices and strands: 0 residues in 0 chains, 3602 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3620 seeds are put forward Round 1: 160 peptides, 35 chains. Longest chain 8 peptides. Score 0.251 Round 2: 195 peptides, 37 chains. Longest chain 12 peptides. Score 0.354 Round 3: 202 peptides, 36 chains. Longest chain 14 peptides. Score 0.395 Round 4: 203 peptides, 36 chains. Longest chain 10 peptides. Score 0.398 Round 5: 198 peptides, 32 chains. Longest chain 12 peptides. Score 0.441 Taking the results from Round 5 Chains 32, Residues 166, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8254 restraints for refining 3521 atoms. 7562 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2429 (Rfree = 0.000) for 3521 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 12: After refmac, R = 0.2236 (Rfree = 0.000) for 3506 atoms. Found 27 (31 requested) and removed 76 (15 requested) atoms. Cycle 13: After refmac, R = 0.2825 (Rfree = 0.000) for 3451 atoms. Found 31 (31 requested) and removed 39 (15 requested) atoms. Cycle 14: After refmac, R = 0.2127 (Rfree = 0.000) for 3439 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 15: After refmac, R = 0.2246 (Rfree = 0.000) for 3444 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3608 seeds are put forward Round 1: 215 peptides, 42 chains. Longest chain 10 peptides. Score 0.351 Round 2: 231 peptides, 42 chains. Longest chain 13 peptides. Score 0.407 Round 3: 230 peptides, 36 chains. Longest chain 16 peptides. Score 0.489 Round 4: 238 peptides, 39 chains. Longest chain 21 peptides. Score 0.473 Round 5: 230 peptides, 38 chains. Longest chain 14 peptides. Score 0.461 Taking the results from Round 3 Chains 39, Residues 194, Estimated correctness of the model 7.7 % 6 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 7673 restraints for refining 3550 atoms. 6810 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2593 (Rfree = 0.000) for 3550 atoms. Found 31 (31 requested) and removed 63 (15 requested) atoms. Cycle 17: After refmac, R = 0.2380 (Rfree = 0.000) for 3500 atoms. Found 31 (31 requested) and removed 30 (15 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2371 (Rfree = 0.000) for 3490 atoms. Found 31 (31 requested) and removed 32 (15 requested) atoms. Cycle 19: After refmac, R = 0.2063 (Rfree = 0.000) for 3483 atoms. Found 24 (31 requested) and removed 30 (15 requested) atoms. Cycle 20: After refmac, R = 0.2155 (Rfree = 0.000) for 3476 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.02 3.46 Search for helices and strands: 0 residues in 0 chains, 3626 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3641 seeds are put forward Round 1: 170 peptides, 37 chains. Longest chain 9 peptides. Score 0.258 Round 2: 211 peptides, 38 chains. Longest chain 11 peptides. Score 0.397 Round 3: 206 peptides, 38 chains. Longest chain 12 peptides. Score 0.379 Round 4: 212 peptides, 39 chains. Longest chain 13 peptides. Score 0.385 Round 5: 202 peptides, 36 chains. Longest chain 11 peptides. Score 0.395 Taking the results from Round 2 Chains 38, Residues 173, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8027 restraints for refining 3561 atoms. 7299 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2157 (Rfree = 0.000) for 3561 atoms. Found 29 (31 requested) and removed 36 (15 requested) atoms. Cycle 22: After refmac, R = 0.2558 (Rfree = 0.000) for 3544 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 23: After refmac, R = 0.2067 (Rfree = 0.000) for 3522 atoms. Found 30 (31 requested) and removed 19 (15 requested) atoms. Cycle 24: After refmac, R = 0.2083 (Rfree = 0.000) for 3524 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 25: After refmac, R = 0.1948 (Rfree = 0.000) for 3529 atoms. Found 15 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.11 3.56 Search for helices and strands: 0 residues in 0 chains, 3654 seeds are put forward NCS extension: 0 residues added, 3654 seeds are put forward Round 1: 170 peptides, 36 chains. Longest chain 9 peptides. Score 0.275 Round 2: 194 peptides, 36 chains. Longest chain 10 peptides. Score 0.366 Round 3: 193 peptides, 35 chains. Longest chain 11 peptides. Score 0.378 Round 4: 203 peptides, 37 chains. Longest chain 11 peptides. Score 0.383 Round 5: 221 peptides, 40 chains. Longest chain 17 peptides. Score 0.402 Taking the results from Round 5 Chains 42, Residues 181, Estimated correctness of the model 0.0 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8219 restraints for refining 3666 atoms. 7442 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2324 (Rfree = 0.000) for 3666 atoms. Found 19 (32 requested) and removed 32 (16 requested) atoms. Cycle 27: After refmac, R = 0.2117 (Rfree = 0.000) for 3640 atoms. Found 28 (32 requested) and removed 21 (16 requested) atoms. Cycle 28: After refmac, R = 0.2037 (Rfree = 0.000) for 3639 atoms. Found 22 (32 requested) and removed 26 (16 requested) atoms. Cycle 29: After refmac, R = 0.2000 (Rfree = 0.000) for 3634 atoms. Found 20 (32 requested) and removed 18 (16 requested) atoms. Cycle 30: After refmac, R = 0.1974 (Rfree = 0.000) for 3635 atoms. Found 17 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.55 Search for helices and strands: 0 residues in 0 chains, 3740 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3753 seeds are put forward Round 1: 176 peptides, 38 chains. Longest chain 7 peptides. Score 0.266 Round 2: 208 peptides, 40 chains. Longest chain 13 peptides. Score 0.356 Round 3: 201 peptides, 39 chains. Longest chain 12 peptides. Score 0.345 Round 4: 208 peptides, 40 chains. Longest chain 14 peptides. Score 0.356 Round 5: 224 peptides, 40 chains. Longest chain 15 peptides. Score 0.412 Taking the results from Round 5 Chains 40, Residues 184, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8374 restraints for refining 3665 atoms. 7656 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2282 (Rfree = 0.000) for 3665 atoms. Found 20 (32 requested) and removed 22 (16 requested) atoms. Cycle 32: After refmac, R = 0.2065 (Rfree = 0.000) for 3657 atoms. Found 15 (32 requested) and removed 19 (16 requested) atoms. Cycle 33: After refmac, R = 0.2734 (Rfree = 0.000) for 3649 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 34: After refmac, R = 0.2148 (Rfree = 0.000) for 3643 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 35: After refmac, R = 0.1951 (Rfree = 0.000) for 3646 atoms. Found 16 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.54 Search for helices and strands: 0 residues in 0 chains, 3764 seeds are put forward NCS extension: 0 residues added, 3764 seeds are put forward Round 1: 155 peptides, 36 chains. Longest chain 7 peptides. Score 0.214 Round 2: 184 peptides, 36 chains. Longest chain 12 peptides. Score 0.329 Round 3: 190 peptides, 38 chains. Longest chain 11 peptides. Score 0.320 Round 4: 196 peptides, 40 chains. Longest chain 10 peptides. Score 0.311 Round 5: 176 peptides, 35 chains. Longest chain 9 peptides. Score 0.315 Taking the results from Round 2 Chains 36, Residues 148, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8489 restraints for refining 3632 atoms. 7909 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2199 (Rfree = 0.000) for 3632 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 37: After refmac, R = 0.2296 (Rfree = 0.000) for 3632 atoms. Found 32 (32 requested) and removed 24 (16 requested) atoms. Cycle 38: After refmac, R = 0.1996 (Rfree = 0.000) for 3636 atoms. Found 26 (32 requested) and removed 19 (16 requested) atoms. Cycle 39: After refmac, R = 0.1953 (Rfree = 0.000) for 3640 atoms. Found 31 (32 requested) and removed 18 (16 requested) atoms. Cycle 40: After refmac, R = 0.1772 (Rfree = 0.000) for 3651 atoms. Found 8 (32 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.54 Search for helices and strands: 0 residues in 0 chains, 3734 seeds are put forward NCS extension: 0 residues added, 3734 seeds are put forward Round 1: 152 peptides, 34 chains. Longest chain 9 peptides. Score 0.235 Round 2: 188 peptides, 36 chains. Longest chain 11 peptides. Score 0.344 Round 3: 196 peptides, 37 chains. Longest chain 11 peptides. Score 0.358 Round 4: 199 peptides, 39 chains. Longest chain 9 peptides. Score 0.338 Round 5: 182 peptides, 32 chains. Longest chain 13 peptides. Score 0.385 Taking the results from Round 5 Chains 33, Residues 150, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8332 restraints for refining 3666 atoms. 7670 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2257 (Rfree = 0.000) for 3666 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 42: After refmac, R = 0.2323 (Rfree = 0.000) for 3657 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 43: After refmac, R = 0.2156 (Rfree = 0.000) for 3650 atoms. Found 32 (32 requested) and removed 21 (16 requested) atoms. Cycle 44: After refmac, R = 0.2368 (Rfree = 0.000) for 3655 atoms. Found 32 (32 requested) and removed 20 (16 requested) atoms. Cycle 45: After refmac, R = 0.2441 (Rfree = 0.000) for 3663 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 3.56 Search for helices and strands: 0 residues in 0 chains, 3752 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3767 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 9 peptides. Score 0.252 Round 2: 151 peptides, 29 chains. Longest chain 10 peptides. Score 0.316 Round 3: 170 peptides, 30 chains. Longest chain 13 peptides. Score 0.372 Round 4: 153 peptides, 29 chains. Longest chain 8 peptides. Score 0.324 Round 5: 160 peptides, 30 chains. Longest chain 10 peptides. Score 0.334 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 140, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence Sequence coverage is 22 % Consider running further cycles of model building using 2pke-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 238 A and 245 A 30 chains (146 residues) following loop building 5 chains (38 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7099 reflections ( 96.62 % complete ) and 8141 restraints for refining 3666 atoms. 7472 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2507 (Rfree = 0.000) for 3666 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2226 (Rfree = 0.000) for 3636 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2233 (Rfree = 0.000) for 3612 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2420 (Rfree = 0.000) for 3593 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 40.35