null Sun 23 Dec 22:22:46 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 2o5r-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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/2o5r-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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 22:22:54 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/2o5r-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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 443 and 0 Target number of residues in the AU: 443 Target solvent content: 0.7011 Checking the provided sequence file Detected sequence length: 481 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 481 Adjusted target solvent content: 0.68 Input MTZ file: 2o5r-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: 152 Cell parameters: 69.953 69.953 283.945 90.000 90.000 120.000 Input sequence file: 2o5r-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3848 target number of atoms Had to go as low as 1.05 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 Loops will be built when appropriate and at the last cycle Resolution range: 19.992 4.000 Wilson plot Bfac: 123.45 7313 reflections ( 98.89 % complete ) and 0 restraints for refining 4237 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3583 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3773 (Rfree = 0.000) for 4237 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.16 3.24 Search for helices and strands: 0 residues in 0 chains, 4317 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 10 peptides. Score 0.310 Round 2: 242 peptides, 33 chains. Longest chain 23 peptides. Score 0.433 Round 3: 252 peptides, 29 chains. Longest chain 21 peptides. Score 0.489 Round 4: 250 peptides, 29 chains. Longest chain 23 peptides. Score 0.486 Round 5: 269 peptides, 32 chains. Longest chain 17 peptides. Score 0.495 Taking the results from Round 5 Chains 33, Residues 237, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7842 restraints for refining 3422 atoms. 6857 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2932 (Rfree = 0.000) for 3422 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 2: After refmac, R = 0.2775 (Rfree = 0.000) for 3327 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 3: After refmac, R = 0.2593 (Rfree = 0.000) for 3272 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 4: After refmac, R = 0.2618 (Rfree = 0.000) for 3239 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 5: After refmac, R = 0.2496 (Rfree = 0.000) for 3201 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.13 3.21 Search for helices and strands: 0 residues in 0 chains, 3387 seeds are put forward Round 1: 253 peptides, 38 chains. Longest chain 16 peptides. Score 0.409 Round 2: 279 peptides, 33 chains. Longest chain 25 peptides. Score 0.504 Round 3: 271 peptides, 31 chains. Longest chain 22 peptides. Score 0.507 Round 4: 269 peptides, 32 chains. Longest chain 18 peptides. Score 0.495 Round 5: 269 peptides, 30 chains. Longest chain 19 peptides. Score 0.512 Taking the results from Round 5 Chains 33, Residues 239, Estimated correctness of the model 0.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7472 restraints for refining 3474 atoms. 6410 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2839 (Rfree = 0.000) for 3474 atoms. Found 14 (16 requested) and removed 118 (8 requested) atoms. Cycle 7: After refmac, R = 0.2573 (Rfree = 0.000) for 3336 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Cycle 8: After refmac, R = 0.2443 (Rfree = 0.000) for 3307 atoms. Found 14 (15 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 3298 atoms. Found 4 (15 requested) and removed 8 (7 requested) atoms. Cycle 10: After refmac, R = 0.2306 (Rfree = 0.000) for 3283 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.16 3.24 Search for helices and strands: 0 residues in 0 chains, 3396 seeds are put forward Round 1: 243 peptides, 35 chains. Longest chain 15 peptides. Score 0.417 Round 2: 262 peptides, 34 chains. Longest chain 20 peptides. Score 0.464 Round 3: 252 peptides, 32 chains. Longest chain 19 peptides. Score 0.462 Round 4: 279 peptides, 33 chains. Longest chain 22 peptides. Score 0.504 Round 5: 263 peptides, 31 chains. Longest chain 22 peptides. Score 0.492 Taking the results from Round 4 Chains 35, Residues 246, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7276 restraints for refining 3474 atoms. 6191 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2738 (Rfree = 0.000) for 3474 atoms. Found 16 (16 requested) and removed 34 (8 requested) atoms. Cycle 12: After refmac, R = 0.2538 (Rfree = 0.000) for 3419 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 13: After refmac, R = 0.2478 (Rfree = 0.000) for 3404 atoms. Found 7 (16 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.2415 (Rfree = 0.000) for 3391 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2374 (Rfree = 0.000) for 3379 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.17 3.24 Search for helices and strands: 0 residues in 0 chains, 3506 seeds are put forward Round 1: 238 peptides, 35 chains. Longest chain 16 peptides. Score 0.407 Round 2: 265 peptides, 31 chains. Longest chain 21 peptides. Score 0.496 Round 3: 266 peptides, 33 chains. Longest chain 22 peptides. Score 0.480 Round 4: 274 peptides, 31 chains. Longest chain 21 peptides. Score 0.512 Round 5: 274 peptides, 27 chains. Longest chain 25 peptides. Score 0.546 Taking the results from Round 5 Chains 31, Residues 247, Estimated correctness of the model 0.0 % 3 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7157 restraints for refining 3472 atoms. 5998 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2769 (Rfree = 0.000) for 3472 atoms. Found 13 (16 requested) and removed 32 (8 requested) atoms. Cycle 17: After refmac, R = 0.2622 (Rfree = 0.000) for 3395 atoms. Found 12 (16 requested) and removed 11 (8 requested) atoms. Cycle 18: After refmac, R = 0.2571 (Rfree = 0.000) for 3380 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2552 (Rfree = 0.000) for 3369 atoms. Found 8 (16 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.2509 (Rfree = 0.000) for 3360 atoms. Found 2 (15 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.14 3.22 Search for helices and strands: 0 residues in 0 chains, 3467 seeds are put forward Round 1: 235 peptides, 38 chains. Longest chain 13 peptides. Score 0.371 Round 2: 259 peptides, 35 chains. Longest chain 20 peptides. Score 0.449 Round 3: 252 peptides, 34 chains. Longest chain 15 peptides. Score 0.444 Round 4: 262 peptides, 32 chains. Longest chain 19 peptides. Score 0.482 Round 5: 260 peptides, 31 chains. Longest chain 21 peptides. Score 0.487 Taking the results from Round 5 Chains 34, Residues 229, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7572 restraints for refining 3474 atoms. 6569 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2912 (Rfree = 0.000) for 3474 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 22: After refmac, R = 0.2615 (Rfree = 0.000) for 3435 atoms. Found 13 (16 requested) and removed 38 (8 requested) atoms. Cycle 23: After refmac, R = 0.2576 (Rfree = 0.000) for 3398 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 24: After refmac, R = 0.2523 (Rfree = 0.000) for 3397 atoms. Found 7 (16 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.2468 (Rfree = 0.000) for 3388 atoms. Found 3 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.24 3.30 Search for helices and strands: 0 residues in 0 chains, 3515 seeds are put forward Round 1: 218 peptides, 32 chains. Longest chain 18 peptides. Score 0.393 Round 2: 246 peptides, 36 chains. Longest chain 16 peptides. Score 0.414 Round 3: 245 peptides, 31 chains. Longest chain 22 peptides. Score 0.458 Round 4: 245 peptides, 33 chains. Longest chain 19 peptides. Score 0.440 Round 5: 249 peptides, 34 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 3 Chains 31, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7936 restraints for refining 3474 atoms. 7111 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3014 (Rfree = 0.000) for 3474 atoms. Found 13 (16 requested) and removed 118 (8 requested) atoms. Cycle 27: After refmac, R = 0.2866 (Rfree = 0.000) for 3325 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 28: After refmac, R = 0.2640 (Rfree = 0.000) for 3314 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.2629 (Rfree = 0.000) for 3302 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.2541 (Rfree = 0.000) for 3296 atoms. Found 12 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.20 3.27 Search for helices and strands: 0 residues in 0 chains, 3496 seeds are put forward Round 1: 217 peptides, 34 chains. Longest chain 21 peptides. Score 0.371 Round 2: 247 peptides, 31 chains. Longest chain 20 peptides. Score 0.462 Round 3: 239 peptides, 31 chains. Longest chain 16 peptides. Score 0.446 Round 4: 264 peptides, 36 chains. Longest chain 16 peptides. Score 0.450 Round 5: 248 peptides, 32 chains. Longest chain 21 peptides. Score 0.455 Taking the results from Round 2 Chains 31, Residues 216, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7628 restraints for refining 3417 atoms. 6795 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2800 (Rfree = 0.000) for 3417 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 32: After refmac, R = 0.2547 (Rfree = 0.000) for 3399 atoms. Found 16 (16 requested) and removed 98 (8 requested) atoms. Cycle 33: After refmac, R = 0.2448 (Rfree = 0.000) for 3305 atoms. Found 13 (15 requested) and removed 256 (7 requested) atoms. Cycle 34: After refmac, R = 0.2635 (Rfree = 0.000) for 3055 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.2619 (Rfree = 0.000) for 3049 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.13 3.21 Search for helices and strands: 0 residues in 0 chains, 3185 seeds are put forward Round 1: 232 peptides, 42 chains. Longest chain 11 peptides. Score 0.326 Round 2: 243 peptides, 35 chains. Longest chain 16 peptides. Score 0.417 Round 3: 244 peptides, 37 chains. Longest chain 15 peptides. Score 0.400 Round 4: 257 peptides, 36 chains. Longest chain 18 peptides. Score 0.436 Round 5: 244 peptides, 36 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 4 Chains 36, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7466 restraints for refining 3376 atoms. 6618 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2637 (Rfree = 0.000) for 3376 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 37: After refmac, R = 0.2511 (Rfree = 0.000) for 3351 atoms. Found 6 (16 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.2518 (Rfree = 0.000) for 3331 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. Cycle 39: After refmac, R = 0.2466 (Rfree = 0.000) for 3314 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 40: After refmac, R = 0.2332 (Rfree = 0.000) for 3309 atoms. Found 7 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.17 3.24 Search for helices and strands: 0 residues in 0 chains, 3450 seeds are put forward Round 1: 211 peptides, 35 chains. Longest chain 14 peptides. Score 0.348 Round 2: 231 peptides, 35 chains. Longest chain 14 peptides. Score 0.392 Round 3: 235 peptides, 35 chains. Longest chain 16 peptides. Score 0.400 Round 4: 241 peptides, 35 chains. Longest chain 19 peptides. Score 0.413 Round 5: 242 peptides, 36 chains. Longest chain 17 peptides. Score 0.405 Taking the results from Round 4 Chains 36, Residues 206, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7313 reflections ( 98.89 % complete ) and 7793 restraints for refining 3474 atoms. 6967 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2824 (Rfree = 0.000) for 3474 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 42: After refmac, R = 0.2644 (Rfree = 0.000) for 3442 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 43: After refmac, R = 0.2507 (Rfree = 0.000) for 3429 atoms. Found 12 (16 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.2368 (Rfree = 0.000) for 3401 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.2366 (Rfree = 0.000) for 3387 atoms. Found 3 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.16 3.24 Search for helices and strands: 0 residues in 0 chains, 3531 seeds are put forward Round 1: 174 peptides, 31 chains. Longest chain 9 peptides. Score 0.303 Round 2: 216 peptides, 32 chains. Longest chain 15 peptides. Score 0.389 Round 3: 223 peptides, 35 chains. Longest chain 14 peptides. Score 0.375 Round 4: 221 peptides, 32 chains. Longest chain 14 peptides. Score 0.400 Round 5: 219 peptides, 30 chains. Longest chain 21 peptides. Score 0.415 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 189, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2o5r-4_warpNtrace.pdb as input Building loops using Loopy2018 33 chains (189 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7313 reflections ( 98.89 % complete ) and 7559 restraints for refining 3474 atoms. 6732 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2757 (Rfree = 0.000) for 3474 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2560 (Rfree = 0.000) for 3447 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2518 (Rfree = 0.000) for 3430 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2511 (Rfree = 0.000) for 3417 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:21:38 GMT 2018 Job finished. TimeTaking 58.86 Used memory is bytes: 16667264