Sun 23 Dec 22:22:59 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 2f4p-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4p-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-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/2f4p-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-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 22:23:07 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/2f4p-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-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 367 and 0 Target number of residues in the AU: 367 Target solvent content: 0.6456 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-4.0-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.65 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: 21.543 4.001 Wilson plot Bfac: 75.05 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4616 reflections ( 99.29 % complete ) and 0 restraints for refining 5208 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3512 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3433 (Rfree = 0.000) for 5208 atoms. Found 23 (24 requested) and removed 72 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.30 4.72 Search for helices and strands: 0 residues in 0 chains, 5217 seeds are put forward NCS extension: 0 residues added, 5217 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 7 peptides. Score 0.218 Round 2: 181 peptides, 35 chains. Longest chain 10 peptides. Score 0.308 Round 3: 195 peptides, 35 chains. Longest chain 10 peptides. Score 0.352 Round 4: 198 peptides, 34 chains. Longest chain 10 peptides. Score 0.375 Round 5: 207 peptides, 35 chains. Longest chain 12 peptides. Score 0.388 Taking the results from Round 5 Chains 35, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 10144 restraints for refining 4120 atoms. 9491 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3211 (Rfree = 0.000) for 4120 atoms. Found 18 (19 requested) and removed 57 (9 requested) atoms. Cycle 2: After refmac, R = 0.3085 (Rfree = 0.000) for 4009 atoms. Found 19 (19 requested) and removed 54 (9 requested) atoms. Cycle 3: After refmac, R = 0.2770 (Rfree = 0.000) for 3918 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 4: After refmac, R = 0.2976 (Rfree = 0.000) for 3863 atoms. Found 18 (18 requested) and removed 43 (9 requested) atoms. Cycle 5: After refmac, R = 0.2889 (Rfree = 0.000) for 3805 atoms. Found 18 (18 requested) and removed 36 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 3.98 Search for helices and strands: 0 residues in 0 chains, 3898 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3909 seeds are put forward Round 1: 159 peptides, 36 chains. Longest chain 8 peptides. Score 0.221 Round 2: 200 peptides, 39 chains. Longest chain 13 peptides. Score 0.315 Round 3: 216 peptides, 41 chains. Longest chain 12 peptides. Score 0.338 Round 4: 236 peptides, 39 chains. Longest chain 14 peptides. Score 0.422 Round 5: 217 peptides, 38 chains. Longest chain 15 peptides. Score 0.380 Taking the results from Round 4 Chains 39, Residues 197, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7994 restraints for refining 3554 atoms. 7231 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2907 (Rfree = 0.000) for 3554 atoms. Found 16 (16 requested) and removed 37 (8 requested) atoms. Cycle 7: After refmac, R = 0.2807 (Rfree = 0.000) for 3464 atoms. Found 16 (16 requested) and removed 39 (8 requested) atoms. Cycle 8: After refmac, R = 0.2766 (Rfree = 0.000) for 3399 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 9: After refmac, R = 0.2287 (Rfree = 0.000) for 3371 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 10: After refmac, R = 0.2646 (Rfree = 0.000) for 3355 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 3454 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3467 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 9 peptides. Score 0.274 Round 2: 218 peptides, 41 chains. Longest chain 9 peptides. Score 0.344 Round 3: 232 peptides, 41 chains. Longest chain 14 peptides. Score 0.386 Round 4: 237 peptides, 39 chains. Longest chain 12 peptides. Score 0.425 Round 5: 241 peptides, 42 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 4 Chains 39, Residues 198, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7731 restraints for refining 3526 atoms. 6917 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2805 (Rfree = 0.000) for 3526 atoms. Found 16 (16 requested) and removed 70 (8 requested) atoms. Cycle 12: After refmac, R = 0.2672 (Rfree = 0.000) for 3450 atoms. Found 16 (16 requested) and removed 39 (8 requested) atoms. Cycle 13: After refmac, R = 0.2596 (Rfree = 0.000) for 3390 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 14: After refmac, R = 0.2564 (Rfree = 0.000) for 3359 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 15: After refmac, R = 0.2087 (Rfree = 0.000) for 3330 atoms. Found 12 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 3406 seeds are put forward NCS extension: 0 residues added, 3406 seeds are put forward Round 1: 199 peptides, 40 chains. Longest chain 8 peptides. Score 0.298 Round 2: 223 peptides, 40 chains. Longest chain 13 peptides. Score 0.372 Round 3: 230 peptides, 41 chains. Longest chain 16 peptides. Score 0.380 Round 4: 242 peptides, 40 chains. Longest chain 15 peptides. Score 0.426 Round 5: 233 peptides, 38 chains. Longest chain 17 peptides. Score 0.425 Taking the results from Round 4 Chains 40, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7544 restraints for refining 3451 atoms. 6776 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2716 (Rfree = 0.000) for 3451 atoms. Found 16 (16 requested) and removed 60 (8 requested) atoms. Cycle 17: After refmac, R = 0.2586 (Rfree = 0.000) for 3383 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 18: After refmac, R = 0.2530 (Rfree = 0.000) for 3356 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 19: After refmac, R = 0.2432 (Rfree = 0.000) for 3326 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 20: After refmac, R = 0.2341 (Rfree = 0.000) for 3306 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 3.99 Search for helices and strands: 0 residues in 0 chains, 3396 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3414 seeds are put forward Round 1: 197 peptides, 41 chains. Longest chain 9 peptides. Score 0.279 Round 2: 237 peptides, 40 chains. Longest chain 13 peptides. Score 0.412 Round 3: 223 peptides, 37 chains. Longest chain 18 peptides. Score 0.410 Round 4: 222 peptides, 39 chains. Longest chain 18 peptides. Score 0.382 Round 5: 214 peptides, 32 chains. Longest chain 18 peptides. Score 0.446 Taking the results from Round 5 Chains 32, Residues 182, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8065 restraints for refining 3579 atoms. 7369 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2782 (Rfree = 0.000) for 3579 atoms. Found 16 (16 requested) and removed 59 (8 requested) atoms. Cycle 22: After refmac, R = 0.2677 (Rfree = 0.000) for 3511 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 23: After refmac, R = 0.2616 (Rfree = 0.000) for 3473 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 24: After refmac, R = 0.2688 (Rfree = 0.000) for 3445 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 25: After refmac, R = 0.2620 (Rfree = 0.000) for 3401 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.64 4.00 Search for helices and strands: 0 residues in 0 chains, 3489 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3513 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 11 peptides. Score 0.245 Round 2: 211 peptides, 40 chains. Longest chain 11 peptides. Score 0.336 Round 3: 229 peptides, 41 chains. Longest chain 13 peptides. Score 0.377 Round 4: 225 peptides, 40 chains. Longest chain 13 peptides. Score 0.378 Round 5: 221 peptides, 37 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 5 Chains 37, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7883 restraints for refining 3529 atoms. 7184 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2594 (Rfree = 0.000) for 3529 atoms. Found 16 (16 requested) and removed 58 (8 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2632 (Rfree = 0.000) for 3456 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 28: After refmac, R = 0.2516 (Rfree = 0.000) for 3419 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 29: After refmac, R = 0.2449 (Rfree = 0.000) for 3386 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 30: After refmac, R = 0.2486 (Rfree = 0.000) for 3373 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.79 4.16 Search for helices and strands: 0 residues in 0 chains, 3464 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3481 seeds are put forward Round 1: 145 peptides, 30 chains. Longest chain 8 peptides. Score 0.259 Round 2: 182 peptides, 32 chains. Longest chain 9 peptides. Score 0.352 Round 3: 177 peptides, 31 chains. Longest chain 10 peptides. Score 0.350 Round 4: 184 peptides, 32 chains. Longest chain 11 peptides. Score 0.359 Round 5: 200 peptides, 30 chains. Longest chain 13 peptides. Score 0.432 Taking the results from Round 5 Chains 31, Residues 170, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7276 restraints for refining 3392 atoms. 6594 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2698 (Rfree = 0.000) for 3392 atoms. Found 16 (16 requested) and removed 50 (8 requested) atoms. Cycle 32: After refmac, R = 0.2502 (Rfree = 0.000) for 3325 atoms. Found 15 (15 requested) and removed 30 (7 requested) atoms. Cycle 33: After refmac, R = 0.2429 (Rfree = 0.000) for 3283 atoms. Found 15 (15 requested) and removed 27 (7 requested) atoms. Cycle 34: After refmac, R = 0.2264 (Rfree = 0.000) for 3257 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 35: After refmac, R = 0.2436 (Rfree = 0.000) for 3237 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 4.06 Search for helices and strands: 0 residues in 0 chains, 3331 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3345 seeds are put forward Round 1: 166 peptides, 35 chains. Longest chain 10 peptides. Score 0.259 Round 2: 187 peptides, 35 chains. Longest chain 19 peptides. Score 0.328 Round 3: 176 peptides, 31 chains. Longest chain 10 peptides. Score 0.347 Round 4: 186 peptides, 28 chains. Longest chain 18 peptides. Score 0.417 Round 5: 193 peptides, 32 chains. Longest chain 11 peptides. Score 0.386 Taking the results from Round 4 Chains 28, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7073 restraints for refining 3246 atoms. 6469 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2732 (Rfree = 0.000) for 3246 atoms. Found 15 (15 requested) and removed 39 (7 requested) atoms. Cycle 37: After refmac, R = 0.2582 (Rfree = 0.000) for 3206 atoms. Found 15 (15 requested) and removed 30 (7 requested) atoms. Cycle 38: After refmac, R = 0.2407 (Rfree = 0.000) for 3173 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 39: After refmac, R = 0.2305 (Rfree = 0.000) for 3159 atoms. Found 15 (15 requested) and removed 20 (7 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2254 (Rfree = 0.000) for 3144 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.99 Search for helices and strands: 0 residues in 0 chains, 3234 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 3261 seeds are put forward Round 1: 134 peptides, 29 chains. Longest chain 9 peptides. Score 0.235 Round 2: 173 peptides, 32 chains. Longest chain 10 peptides. Score 0.324 Round 3: 174 peptides, 33 chains. Longest chain 10 peptides. Score 0.313 Round 4: 192 peptides, 36 chains. Longest chain 11 peptides. Score 0.330 Round 5: 190 peptides, 32 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 5 Chains 32, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7218 restraints for refining 3322 atoms. 6618 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2873 (Rfree = 0.000) for 3322 atoms. Found 15 (15 requested) and removed 41 (7 requested) atoms. Cycle 42: After refmac, R = 0.2594 (Rfree = 0.000) for 3276 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 43: After refmac, R = 0.2577 (Rfree = 0.000) for 3243 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 44: After refmac, R = 0.2316 (Rfree = 0.000) for 3223 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 45: After refmac, R = 0.1944 (Rfree = 0.000) for 3208 atoms. Found 15 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 3309 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3330 seeds are put forward Round 1: 117 peptides, 26 chains. Longest chain 7 peptides. Score 0.218 Round 2: 141 peptides, 29 chains. Longest chain 10 peptides. Score 0.260 Round 3: 156 peptides, 27 chains. Longest chain 15 peptides. Score 0.339 Round 4: 158 peptides, 27 chains. Longest chain 16 peptides. Score 0.346 Round 5: 158 peptides, 25 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 133, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2f4p-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4616 reflections ( 99.29 % complete ) and 7230 restraints for refining 3343 atoms. 6678 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2604 (Rfree = 0.000) for 3343 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2529 (Rfree = 0.000) for 3312 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2675 (Rfree = 0.000) for 3292 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2426 (Rfree = 0.000) for 3264 atoms. TimeTaking 59.92