null Sun 23 Dec 23:52:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2gb5-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-parrot-mrncs ############### 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 23:53:17 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-4.0-parrot-mrncs/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 367 and 0 Target number of residues in the AU: 367 Target solvent content: 0.6627 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-4.0-parrot-mrncs.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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4304 target number of atoms Had to go as low as 0.85 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: 49.644 4.000 Wilson plot Bfac: 86.93 5306 reflections ( 99.23 % complete ) and 0 restraints for refining 4739 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3360 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3225 (Rfree = 0.000) for 4739 atoms. Found 12 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 4796 seeds are put forward NCS extension: 0 residues added, 4796 seeds are put forward Round 1: 139 peptides, 31 chains. Longest chain 9 peptides. Score 0.221 Round 2: 174 peptides, 31 chains. Longest chain 11 peptides. Score 0.335 Round 3: 196 peptides, 36 chains. Longest chain 12 peptides. Score 0.336 Round 4: 219 peptides, 38 chains. Longest chain 17 peptides. Score 0.378 Round 5: 241 peptides, 41 chains. Longest chain 17 peptides. Score 0.403 Taking the results from Round 5 Chains 41, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 9478 restraints for refining 3886 atoms. 8719 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2987 (Rfree = 0.000) for 3886 atoms. Found 9 (18 requested) and removed 29 (9 requested) atoms. Cycle 2: After refmac, R = 0.3015 (Rfree = 0.000) for 3794 atoms. Found 5 (18 requested) and removed 23 (9 requested) atoms. Cycle 3: After refmac, R = 0.3013 (Rfree = 0.000) for 3722 atoms. Found 7 (17 requested) and removed 15 (8 requested) atoms. Cycle 4: After refmac, R = 0.2941 (Rfree = 0.000) for 3673 atoms. Found 8 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.2581 (Rfree = 0.000) for 3640 atoms. Found 5 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.78 Search for helices and strands: 0 residues in 0 chains, 3712 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3731 seeds are put forward Round 1: 156 peptides, 33 chains. Longest chain 12 peptides. Score 0.251 Round 2: 205 peptides, 38 chains. Longest chain 19 peptides. Score 0.337 Round 3: 227 peptides, 38 chains. Longest chain 20 peptides. Score 0.400 Round 4: 234 peptides, 38 chains. Longest chain 20 peptides. Score 0.419 Round 5: 233 peptides, 37 chains. Longest chain 21 peptides. Score 0.428 Taking the results from Round 5 Chains 37, Residues 196, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7754 restraints for refining 3391 atoms. 7007 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2824 (Rfree = 0.000) for 3391 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 7: After refmac, R = 0.2729 (Rfree = 0.000) for 3347 atoms. Found 11 (16 requested) and removed 18 (8 requested) atoms. Cycle 8: After refmac, R = 0.2651 (Rfree = 0.000) for 3315 atoms. Found 12 (15 requested) and removed 13 (7 requested) atoms. Cycle 9: After refmac, R = 0.2589 (Rfree = 0.000) for 3284 atoms. Found 8 (15 requested) and removed 14 (7 requested) atoms. Cycle 10: After refmac, R = 0.2739 (Rfree = 0.000) for 3261 atoms. Found 11 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.74 Search for helices and strands: 0 residues in 0 chains, 3384 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3418 seeds are put forward Round 1: 182 peptides, 35 chains. Longest chain 12 peptides. Score 0.307 Round 2: 233 peptides, 40 chains. Longest chain 12 peptides. Score 0.392 Round 3: 212 peptides, 35 chains. Longest chain 15 peptides. Score 0.395 Round 4: 219 peptides, 36 chains. Longest chain 12 peptides. Score 0.402 Round 5: 231 peptides, 37 chains. Longest chain 16 peptides. Score 0.423 Taking the results from Round 5 Chains 37, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7628 restraints for refining 3410 atoms. 6889 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2758 (Rfree = 0.000) for 3410 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 12: After refmac, R = 0.2573 (Rfree = 0.000) for 3362 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 13: After refmac, R = 0.2381 (Rfree = 0.000) for 3342 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2454 (Rfree = 0.000) for 3327 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.2532 (Rfree = 0.000) for 3304 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 3427 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3454 seeds are put forward Round 1: 185 peptides, 38 chains. Longest chain 8 peptides. Score 0.276 Round 2: 226 peptides, 39 chains. Longest chain 12 peptides. Score 0.385 Round 3: 229 peptides, 37 chains. Longest chain 18 peptides. Score 0.417 Round 4: 225 peptides, 37 chains. Longest chain 14 peptides. Score 0.406 Round 5: 219 peptides, 36 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 3 Chains 37, Residues 192, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7265 restraints for refining 3291 atoms. 6534 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2626 (Rfree = 0.000) for 3291 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Cycle 17: After refmac, R = 0.2508 (Rfree = 0.000) for 3259 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 18: After refmac, R = 0.2495 (Rfree = 0.000) for 3241 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2566 (Rfree = 0.000) for 3232 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2462 (Rfree = 0.000) for 3225 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 3338 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3366 seeds are put forward Round 1: 154 peptides, 29 chains. Longest chain 13 peptides. Score 0.300 Round 2: 209 peptides, 35 chains. Longest chain 16 peptides. Score 0.386 Round 3: 220 peptides, 38 chains. Longest chain 16 peptides. Score 0.380 Round 4: 235 peptides, 38 chains. Longest chain 15 peptides. Score 0.422 Round 5: 208 peptides, 33 chains. Longest chain 18 peptides. Score 0.408 Taking the results from Round 4 Chains 38, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7518 restraints for refining 3347 atoms. 6768 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2597 (Rfree = 0.000) for 3347 atoms. Found 14 (15 requested) and removed 20 (7 requested) atoms. Cycle 22: After refmac, R = 0.2534 (Rfree = 0.000) for 3322 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 23: After refmac, R = 0.2451 (Rfree = 0.000) for 3293 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 24: After refmac, R = 0.2464 (Rfree = 0.000) for 3279 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2521 (Rfree = 0.000) for 3269 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 3345 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3364 seeds are put forward Round 1: 172 peptides, 37 chains. Longest chain 7 peptides. Score 0.248 Round 2: 195 peptides, 35 chains. Longest chain 13 peptides. Score 0.346 Round 3: 208 peptides, 36 chains. Longest chain 16 peptides. Score 0.371 Round 4: 197 peptides, 32 chains. Longest chain 14 peptides. Score 0.389 Round 5: 198 peptides, 31 chains. Longest chain 17 peptides. Score 0.405 Taking the results from Round 5 Chains 32, Residues 167, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7741 restraints for refining 3506 atoms. 7011 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2831 (Rfree = 0.000) for 3506 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 27: After refmac, R = 0.2561 (Rfree = 0.000) for 3467 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 28: After refmac, R = 0.2370 (Rfree = 0.000) for 3439 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 29: After refmac, R = 0.2510 (Rfree = 0.000) for 3423 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 30: After refmac, R = 0.2468 (Rfree = 0.000) for 3412 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 3469 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 3494 seeds are put forward Round 1: 147 peptides, 32 chains. Longest chain 8 peptides. Score 0.234 Round 2: 191 peptides, 36 chains. Longest chain 10 peptides. Score 0.321 Round 3: 190 peptides, 37 chains. Longest chain 11 peptides. Score 0.305 Round 4: 197 peptides, 33 chains. Longest chain 12 peptides. Score 0.377 Round 5: 183 peptides, 34 chains. Longest chain 11 peptides. Score 0.323 Taking the results from Round 4 Chains 33, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7782 restraints for refining 3441 atoms. 7159 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2828 (Rfree = 0.000) for 3441 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 32: After refmac, R = 0.2647 (Rfree = 0.000) for 3390 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 33: After refmac, R = 0.2669 (Rfree = 0.000) for 3359 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 34: After refmac, R = 0.2633 (Rfree = 0.000) for 3345 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.2640 (Rfree = 0.000) for 3337 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 3429 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3444 seeds are put forward Round 1: 143 peptides, 33 chains. Longest chain 6 peptides. Score 0.206 Round 2: 165 peptides, 31 chains. Longest chain 8 peptides. Score 0.307 Round 3: 181 peptides, 34 chains. Longest chain 9 peptides. Score 0.317 Round 4: 174 peptides, 30 chains. Longest chain 9 peptides. Score 0.348 Round 5: 178 peptides, 34 chains. Longest chain 13 peptides. Score 0.307 Taking the results from Round 4 Chains 30, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7206 restraints for refining 3239 atoms. 6660 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2590 (Rfree = 0.000) for 3239 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 37: After refmac, R = 0.2537 (Rfree = 0.000) for 3216 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 38: After refmac, R = 0.2463 (Rfree = 0.000) for 3198 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 39: After refmac, R = 0.2435 (Rfree = 0.000) for 3192 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.2369 (Rfree = 0.000) for 3183 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 3.64 Search for helices and strands: 0 residues in 0 chains, 3274 seeds are put forward NCS extension: 0 residues added, 3274 seeds are put forward Round 1: 150 peptides, 34 chains. Longest chain 9 peptides. Score 0.216 Round 2: 177 peptides, 35 chains. Longest chain 9 peptides. Score 0.291 Round 3: 171 peptides, 32 chains. Longest chain 9 peptides. Score 0.312 Round 4: 174 peptides, 30 chains. Longest chain 13 peptides. Score 0.348 Round 5: 182 peptides, 32 chains. Longest chain 10 peptides. Score 0.346 Taking the results from Round 4 Chains 30, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.23 % complete ) and 7616 restraints for refining 3332 atoms. 7070 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2784 (Rfree = 0.000) for 3332 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 42: After refmac, R = 0.2603 (Rfree = 0.000) for 3301 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 43: After refmac, R = 0.2551 (Rfree = 0.000) for 3285 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.2580 (Rfree = 0.000) for 3280 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.2495 (Rfree = 0.000) for 3272 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.63 Search for helices and strands: 0 residues in 0 chains, 3375 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3396 seeds are put forward Round 1: 114 peptides, 27 chains. Longest chain 6 peptides. Score 0.190 Round 2: 139 peptides, 31 chains. Longest chain 6 peptides. Score 0.221 Round 3: 152 peptides, 29 chains. Longest chain 10 peptides. Score 0.293 Round 4: 145 peptides, 29 chains. Longest chain 10 peptides. Score 0.270 Round 5: 147 peptides, 29 chains. Longest chain 8 peptides. Score 0.277 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gb5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5306 reflections ( 99.23 % complete ) and 6661 restraints for refining 3056 atoms. 6198 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2652 (Rfree = 0.000) for 3056 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2550 (Rfree = 0.000) for 3034 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2524 (Rfree = 0.000) for 3009 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2331 (Rfree = 0.000) for 2994 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:32:27 GMT 2018 Job finished. TimeTaking 99.54 Used memory is bytes: 14037904