Mon 24 Dec 07:38:56 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 2a9v-2.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-2.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2a9v-2.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-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/2a9v-2.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-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 07:39:01 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/2a9v-2.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-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 661 and 0 Target number of residues in the AU: 661 Target solvent content: 0.5129 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-2.2-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: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-2.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 6784 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 1 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: 137.806 2.200 Wilson plot Bfac: 26.11 33709 reflections ( 87.11 % complete ) and 0 restraints for refining 7477 atoms. Observations/parameters ratio is 1.13 ------------------------------------------------------ Starting model: R = 0.3857 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3302 (Rfree = 0.000) for 7477 atoms. Found 110 (195 requested) and removed 173 (97 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.28 2.68 NCS extension: 0 residues added, 7414 seeds are put forward Round 1: 271 peptides, 61 chains. Longest chain 8 peptides. Score 0.236 Round 2: 298 peptides, 62 chains. Longest chain 8 peptides. Score 0.292 Round 3: 310 peptides, 61 chains. Longest chain 10 peptides. Score 0.329 Round 4: 318 peptides, 55 chains. Longest chain 17 peptides. Score 0.404 Round 5: 311 peptides, 50 chains. Longest chain 17 peptides. Score 0.436 Taking the results from Round 5 Chains 50, Residues 261, Estimated correctness of the model 66.3 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 14575 restraints for refining 6476 atoms. 13535 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3389 (Rfree = 0.000) for 6476 atoms. Found 114 (169 requested) and removed 94 (84 requested) atoms. Cycle 2: After refmac, R = 0.3168 (Rfree = 0.000) for 6490 atoms. Found 73 (169 requested) and removed 84 (84 requested) atoms. Cycle 3: After refmac, R = 0.3051 (Rfree = 0.000) for 6467 atoms. Found 61 (169 requested) and removed 84 (84 requested) atoms. Cycle 4: After refmac, R = 0.2996 (Rfree = 0.000) for 6437 atoms. Found 83 (168 requested) and removed 84 (84 requested) atoms. Cycle 5: After refmac, R = 0.2957 (Rfree = 0.000) for 6429 atoms. Found 73 (168 requested) and removed 84 (84 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.18 2.57 NCS extension: 0 residues added, 6458 seeds are put forward Round 1: 313 peptides, 58 chains. Longest chain 21 peptides. Score 0.365 Round 2: 334 peptides, 53 chains. Longest chain 22 peptides. Score 0.456 Round 3: 344 peptides, 53 chains. Longest chain 24 peptides. Score 0.476 Round 4: 353 peptides, 57 chains. Longest chain 24 peptides. Score 0.459 Round 5: 364 peptides, 61 chains. Longest chain 19 peptides. Score 0.447 Taking the results from Round 3 Chains 54, Residues 291, Estimated correctness of the model 70.5 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 14376 restraints for refining 6477 atoms. 13170 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3083 (Rfree = 0.000) for 6477 atoms. Found 115 (169 requested) and removed 89 (84 requested) atoms. Cycle 7: After refmac, R = 0.2972 (Rfree = 0.000) for 6498 atoms. Found 86 (169 requested) and removed 84 (84 requested) atoms. Cycle 8: After refmac, R = 0.2844 (Rfree = 0.000) for 6497 atoms. Found 75 (169 requested) and removed 84 (84 requested) atoms. Cycle 9: After refmac, R = 0.2837 (Rfree = 0.000) for 6482 atoms. Found 73 (169 requested) and removed 84 (84 requested) atoms. Cycle 10: After refmac, R = 0.2772 (Rfree = 0.000) for 6470 atoms. Found 81 (168 requested) and removed 62 (84 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.17 2.55 NCS extension: 4 residues added (0 deleted due to clashes), 6520 seeds are put forward Round 1: 315 peptides, 59 chains. Longest chain 19 peptides. Score 0.360 Round 2: 322 peptides, 55 chains. Longest chain 20 peptides. Score 0.413 Round 3: 340 peptides, 54 chains. Longest chain 16 peptides. Score 0.459 Round 4: 345 peptides, 56 chains. Longest chain 21 peptides. Score 0.452 Round 5: 347 peptides, 54 chains. Longest chain 22 peptides. Score 0.473 Taking the results from Round 5 Chains 55, Residues 293, Estimated correctness of the model 70.2 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 14149 restraints for refining 6477 atoms. 12991 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2950 (Rfree = 0.000) for 6477 atoms. Found 120 (169 requested) and removed 85 (84 requested) atoms. Cycle 12: After refmac, R = 0.2754 (Rfree = 0.000) for 6511 atoms. Found 88 (169 requested) and removed 79 (84 requested) atoms. Cycle 13: After refmac, R = 0.2646 (Rfree = 0.000) for 6519 atoms. Found 62 (170 requested) and removed 47 (85 requested) atoms. Cycle 14: After refmac, R = 0.2572 (Rfree = 0.000) for 6532 atoms. Found 81 (170 requested) and removed 34 (85 requested) atoms. Cycle 15: After refmac, R = 0.2557 (Rfree = 0.000) for 6579 atoms. Found 67 (171 requested) and removed 50 (85 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.16 2.54 NCS extension: 0 residues added, 6618 seeds are put forward Round 1: 327 peptides, 57 chains. Longest chain 22 peptides. Score 0.405 Round 2: 333 peptides, 54 chains. Longest chain 14 peptides. Score 0.445 Round 3: 354 peptides, 54 chains. Longest chain 24 peptides. Score 0.487 Round 4: 345 peptides, 54 chains. Longest chain 22 peptides. Score 0.469 Round 5: 345 peptides, 53 chains. Longest chain 24 peptides. Score 0.478 Taking the results from Round 3 Chains 55, Residues 300, Estimated correctness of the model 71.7 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13772 restraints for refining 6477 atoms. 12564 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2725 (Rfree = 0.000) for 6477 atoms. Found 119 (169 requested) and removed 90 (84 requested) atoms. Cycle 17: After refmac, R = 0.2590 (Rfree = 0.000) for 6503 atoms. Found 90 (169 requested) and removed 53 (84 requested) atoms. Cycle 18: After refmac, R = 0.2500 (Rfree = 0.000) for 6539 atoms. Found 91 (170 requested) and removed 42 (85 requested) atoms. Cycle 19: After refmac, R = 0.2440 (Rfree = 0.000) for 6585 atoms. Found 74 (171 requested) and removed 39 (85 requested) atoms. Cycle 20: After refmac, R = 0.2380 (Rfree = 0.000) for 6620 atoms. Found 60 (172 requested) and removed 36 (86 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.15 2.53 NCS extension: 0 residues added, 6669 seeds are put forward Round 1: 303 peptides, 53 chains. Longest chain 12 peptides. Score 0.390 Round 2: 322 peptides, 49 chains. Longest chain 24 peptides. Score 0.467 Round 3: 307 peptides, 50 chains. Longest chain 14 peptides. Score 0.427 Round 4: 311 peptides, 47 chains. Longest chain 15 peptides. Score 0.463 Round 5: 307 peptides, 49 chains. Longest chain 14 peptides. Score 0.436 Taking the results from Round 2 Chains 49, Residues 273, Estimated correctness of the model 69.6 % 3 chains (12 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13888 restraints for refining 6477 atoms. 12820 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2539 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 54 (84 requested) atoms. Cycle 22: After refmac, R = 0.2451 (Rfree = 0.000) for 6592 atoms. Found 106 (172 requested) and removed 53 (86 requested) atoms. Cycle 23: After refmac, R = 0.2376 (Rfree = 0.000) for 6643 atoms. Found 85 (173 requested) and removed 49 (86 requested) atoms. Cycle 24: After refmac, R = 0.2302 (Rfree = 0.000) for 6679 atoms. Found 104 (174 requested) and removed 49 (87 requested) atoms. Cycle 25: After refmac, R = 0.2283 (Rfree = 0.000) for 6732 atoms. Found 91 (175 requested) and removed 60 (87 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.15 2.53 NCS extension: 7 residues added (1 deleted due to clashes), 6795 seeds are put forward Round 1: 299 peptides, 56 chains. Longest chain 13 peptides. Score 0.353 Round 2: 342 peptides, 55 chains. Longest chain 22 peptides. Score 0.455 Round 3: 308 peptides, 48 chains. Longest chain 23 peptides. Score 0.448 Round 4: 323 peptides, 53 chains. Longest chain 17 peptides. Score 0.433 Round 5: 313 peptides, 50 chains. Longest chain 23 peptides. Score 0.440 Taking the results from Round 2 Chains 57, Residues 287, Estimated correctness of the model 68.3 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13537 restraints for refining 6477 atoms. 12406 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2526 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 73 (84 requested) atoms. Cycle 27: After refmac, R = 0.2441 (Rfree = 0.000) for 6570 atoms. Found 114 (171 requested) and removed 39 (85 requested) atoms. Cycle 28: After refmac, R = 0.2334 (Rfree = 0.000) for 6644 atoms. Found 93 (173 requested) and removed 35 (86 requested) atoms. Cycle 29: After refmac, R = 0.2294 (Rfree = 0.000) for 6701 atoms. Found 70 (174 requested) and removed 42 (87 requested) atoms. Cycle 30: After refmac, R = 0.2260 (Rfree = 0.000) for 6729 atoms. Found 93 (175 requested) and removed 41 (87 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.14 2.52 NCS extension: 0 residues added, 6802 seeds are put forward Round 1: 277 peptides, 53 chains. Longest chain 10 peptides. Score 0.331 Round 2: 300 peptides, 50 chains. Longest chain 13 peptides. Score 0.412 Round 3: 300 peptides, 48 chains. Longest chain 13 peptides. Score 0.431 Round 4: 306 peptides, 46 chains. Longest chain 13 peptides. Score 0.462 Round 5: 297 peptides, 46 chains. Longest chain 13 peptides. Score 0.443 Taking the results from Round 4 Chains 46, Residues 260, Estimated correctness of the model 69.1 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13638 restraints for refining 6477 atoms. 12617 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2529 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 41 (84 requested) atoms. Cycle 32: After refmac, R = 0.2378 (Rfree = 0.000) for 6604 atoms. Found 108 (172 requested) and removed 28 (86 requested) atoms. Cycle 33: After refmac, R = 0.2291 (Rfree = 0.000) for 6680 atoms. Found 90 (174 requested) and removed 36 (87 requested) atoms. Cycle 34: After refmac, R = 0.2258 (Rfree = 0.000) for 6733 atoms. Found 63 (175 requested) and removed 51 (87 requested) atoms. Cycle 35: After refmac, R = 0.2217 (Rfree = 0.000) for 6743 atoms. Found 89 (176 requested) and removed 35 (88 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.16 2.54 NCS extension: 0 residues added, 6811 seeds are put forward Round 1: 294 peptides, 55 chains. Longest chain 12 peptides. Score 0.351 Round 2: 298 peptides, 51 chains. Longest chain 11 peptides. Score 0.398 Round 3: 287 peptides, 47 chains. Longest chain 13 peptides. Score 0.412 Round 4: 289 peptides, 48 chains. Longest chain 12 peptides. Score 0.407 Round 5: 278 peptides, 46 chains. Longest chain 12 peptides. Score 0.402 Taking the results from Round 3 Chains 48, Residues 240, Estimated correctness of the model 63.6 % 6 chains (26 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13617 restraints for refining 6477 atoms. 12655 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2477 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 65 (84 requested) atoms. Cycle 37: After refmac, R = 0.2360 (Rfree = 0.000) for 6581 atoms. Found 135 (171 requested) and removed 25 (85 requested) atoms. Cycle 38: After refmac, R = 0.2295 (Rfree = 0.000) for 6687 atoms. Found 73 (174 requested) and removed 58 (87 requested) atoms. Cycle 39: After refmac, R = 0.2269 (Rfree = 0.000) for 6701 atoms. Found 94 (174 requested) and removed 34 (87 requested) atoms. Cycle 40: After refmac, R = 0.2236 (Rfree = 0.000) for 6759 atoms. Found 78 (176 requested) and removed 52 (88 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.16 2.54 NCS extension: 0 residues added, 6804 seeds are put forward Round 1: 244 peptides, 45 chains. Longest chain 12 peptides. Score 0.334 Round 2: 249 peptides, 42 chains. Longest chain 11 peptides. Score 0.376 Round 3: 256 peptides, 41 chains. Longest chain 12 peptides. Score 0.402 Round 4: 269 peptides, 42 chains. Longest chain 12 peptides. Score 0.421 Round 5: 271 peptides, 43 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 4 Chains 43, Residues 227, Estimated correctness of the model 64.6 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 13538 restraints for refining 6477 atoms. 12584 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2448 (Rfree = 0.000) for 6477 atoms. Found 169 (169 requested) and removed 76 (84 requested) atoms. Cycle 42: After refmac, R = 0.2354 (Rfree = 0.000) for 6569 atoms. Found 121 (171 requested) and removed 27 (85 requested) atoms. Cycle 43: After refmac, R = 0.2263 (Rfree = 0.000) for 6660 atoms. Found 75 (173 requested) and removed 28 (86 requested) atoms. Cycle 44: After refmac, R = 0.2213 (Rfree = 0.000) for 6707 atoms. Found 70 (175 requested) and removed 39 (87 requested) atoms. Cycle 45: After refmac, R = 0.2179 (Rfree = 0.000) for 6731 atoms. Found 63 (175 requested) and removed 34 (87 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.17 2.55 NCS extension: 0 residues added, 6774 seeds are put forward Round 1: 282 peptides, 50 chains. Longest chain 13 peptides. Score 0.372 Round 2: 279 peptides, 46 chains. Longest chain 14 peptides. Score 0.404 Round 3: 274 peptides, 44 chains. Longest chain 13 peptides. Score 0.412 Round 4: 270 peptides, 44 chains. Longest chain 12 peptides. Score 0.404 Round 5: 276 peptides, 44 chains. Longest chain 14 peptides. Score 0.417 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 44, Residues 232, Estimated correctness of the model 64.2 % 5 chains (27 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2a9v-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 65 A and 75 A 43 chains (241 residues) following loop building 4 chains (36 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 33709 reflections ( 87.11 % complete ) and 13240 restraints for refining 6477 atoms. 12194 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2513 (Rfree = 0.000) for 6477 atoms. Found 0 (169 requested) and removed 14 (84 requested) atoms. Cycle 47: After refmac, R = 0.2423 (Rfree = 0.000) for 6463 atoms. Found 0 (168 requested) and removed 1 (84 requested) atoms. Cycle 48: After refmac, R = 0.2385 (Rfree = 0.000) for 6460 atoms. Found 0 (168 requested) and removed 5 (84 requested) atoms. Cycle 49: After refmac, R = 0.2389 (Rfree = 0.000) for 6455 atoms. TimeTaking 61.63