Mon 24 Dec 00:59:56 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 2gfg-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gfg-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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/2gfg-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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 ============================================================ Mon 24 Dec 01:00:01 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/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gfg-2.1-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 513 and 0 Target number of residues in the AU: 513 Target solvent content: 0.5408 Checking the provided sequence file Detected sequence length: 193 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 579 Adjusted target solvent content: 0.48 Input MTZ file: 2gfg-2.1-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: 19 Cell parameters: 43.030 74.690 188.130 90.000 90.000 90.000 Input sequence file: 2gfg-2.1-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4632 target number of atoms Had to go as low as 0.55 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: 94.065 2.120 Wilson plot Bfac: 32.97 34827 reflections ( 98.30 % complete ) and 0 restraints for refining 5110 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Starting model: R = 0.3945 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3412 (Rfree = 0.000) for 5110 atoms. Found 69 (148 requested) and removed 90 (74 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.37 2.43 NCS extension: 0 residues added, 5089 seeds are put forward Round 1: 248 peptides, 52 chains. Longest chain 11 peptides. Score 0.288 Round 2: 286 peptides, 48 chains. Longest chain 15 peptides. Score 0.436 Round 3: 306 peptides, 49 chains. Longest chain 15 peptides. Score 0.475 Round 4: 303 peptides, 48 chains. Longest chain 17 peptides. Score 0.478 Round 5: 297 peptides, 45 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 5 Chains 46, Residues 252, Estimated correctness of the model 75.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9577 restraints for refining 4447 atoms. 8582 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3680 (Rfree = 0.000) for 4447 atoms. Found 73 (129 requested) and removed 74 (64 requested) atoms. Cycle 2: After refmac, R = 0.3468 (Rfree = 0.000) for 4430 atoms. Found 59 (129 requested) and removed 67 (64 requested) atoms. Cycle 3: After refmac, R = 0.3280 (Rfree = 0.000) for 4409 atoms. Found 32 (128 requested) and removed 65 (64 requested) atoms. Cycle 4: After refmac, R = 0.3178 (Rfree = 0.000) for 4368 atoms. Found 39 (126 requested) and removed 59 (63 requested) atoms. Cycle 5: After refmac, R = 0.3096 (Rfree = 0.000) for 4344 atoms. Found 35 (126 requested) and removed 29 (63 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.31 2.37 NCS extension: 14 residues added (0 deleted due to clashes), 4397 seeds are put forward Round 1: 264 peptides, 42 chains. Longest chain 16 peptides. Score 0.447 Round 2: 278 peptides, 41 chains. Longest chain 16 peptides. Score 0.492 Round 3: 294 peptides, 41 chains. Longest chain 16 peptides. Score 0.528 Round 4: 292 peptides, 39 chains. Longest chain 17 peptides. Score 0.544 Round 5: 291 peptides, 43 chains. Longest chain 14 peptides. Score 0.501 Taking the results from Round 4 Chains 39, Residues 253, Estimated correctness of the model 79.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9695 restraints for refining 4404 atoms. 8722 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3277 (Rfree = 0.000) for 4404 atoms. Found 66 (127 requested) and removed 63 (63 requested) atoms. Cycle 7: After refmac, R = 0.3105 (Rfree = 0.000) for 4407 atoms. Found 54 (127 requested) and removed 49 (63 requested) atoms. Cycle 8: After refmac, R = 0.3024 (Rfree = 0.000) for 4410 atoms. Found 28 (128 requested) and removed 24 (64 requested) atoms. Cycle 9: After refmac, R = 0.2966 (Rfree = 0.000) for 4410 atoms. Found 37 (128 requested) and removed 30 (64 requested) atoms. Cycle 10: After refmac, R = 0.2917 (Rfree = 0.000) for 4416 atoms. Found 32 (128 requested) and removed 11 (64 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.28 2.34 NCS extension: 20 residues added (0 deleted due to clashes), 4467 seeds are put forward Round 1: 262 peptides, 42 chains. Longest chain 16 peptides. Score 0.442 Round 2: 291 peptides, 39 chains. Longest chain 18 peptides. Score 0.542 Round 3: 286 peptides, 39 chains. Longest chain 18 peptides. Score 0.531 Round 4: 290 peptides, 39 chains. Longest chain 19 peptides. Score 0.539 Round 5: 297 peptides, 41 chains. Longest chain 20 peptides. Score 0.535 Taking the results from Round 2 Chains 40, Residues 252, Estimated correctness of the model 79.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9453 restraints for refining 4437 atoms. 8447 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3114 (Rfree = 0.000) for 4437 atoms. Found 83 (128 requested) and removed 65 (64 requested) atoms. Cycle 12: After refmac, R = 0.2955 (Rfree = 0.000) for 4454 atoms. Found 49 (129 requested) and removed 25 (64 requested) atoms. Cycle 13: After refmac, R = 0.2903 (Rfree = 0.000) for 4477 atoms. Found 37 (129 requested) and removed 34 (64 requested) atoms. Cycle 14: After refmac, R = 0.2849 (Rfree = 0.000) for 4480 atoms. Found 33 (129 requested) and removed 22 (64 requested) atoms. Cycle 15: After refmac, R = 0.2815 (Rfree = 0.000) for 4490 atoms. Found 18 (130 requested) and removed 12 (65 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.29 2.35 NCS extension: 20 residues added (1 deleted due to clashes), 4529 seeds are put forward Round 1: 276 peptides, 46 chains. Longest chain 16 peptides. Score 0.433 Round 2: 267 peptides, 37 chains. Longest chain 15 peptides. Score 0.508 Round 3: 279 peptides, 40 chains. Longest chain 13 peptides. Score 0.504 Round 4: 288 peptides, 39 chains. Longest chain 16 peptides. Score 0.535 Round 5: 285 peptides, 40 chains. Longest chain 16 peptides. Score 0.518 Taking the results from Round 4 Chains 39, Residues 249, Estimated correctness of the model 79.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9506 restraints for refining 4448 atoms. 8549 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3097 (Rfree = 0.000) for 4448 atoms. Found 95 (129 requested) and removed 63 (64 requested) atoms. Cycle 17: After refmac, R = 0.2927 (Rfree = 0.000) for 4476 atoms. Found 57 (129 requested) and removed 32 (64 requested) atoms. Cycle 18: After refmac, R = 0.2813 (Rfree = 0.000) for 4495 atoms. Found 41 (130 requested) and removed 15 (65 requested) atoms. Cycle 19: After refmac, R = 0.2740 (Rfree = 0.000) for 4516 atoms. Found 20 (131 requested) and removed 14 (65 requested) atoms. Cycle 20: After refmac, R = 0.2690 (Rfree = 0.000) for 4517 atoms. Found 23 (131 requested) and removed 8 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.29 2.35 NCS extension: 14 residues added (4 deleted due to clashes), 4557 seeds are put forward Round 1: 244 peptides, 39 chains. Longest chain 18 peptides. Score 0.429 Round 2: 264 peptides, 38 chains. Longest chain 15 peptides. Score 0.490 Round 3: 273 peptides, 39 chains. Longest chain 16 peptides. Score 0.501 Round 4: 270 peptides, 37 chains. Longest chain 13 peptides. Score 0.514 Round 5: 288 peptides, 38 chains. Longest chain 17 peptides. Score 0.545 Taking the results from Round 5 Chains 38, Residues 250, Estimated correctness of the model 79.8 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9334 restraints for refining 4448 atoms. 8344 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3001 (Rfree = 0.000) for 4448 atoms. Found 95 (129 requested) and removed 45 (64 requested) atoms. Cycle 22: After refmac, R = 0.2839 (Rfree = 0.000) for 4495 atoms. Found 47 (130 requested) and removed 24 (65 requested) atoms. Cycle 23: After refmac, R = 0.2755 (Rfree = 0.000) for 4512 atoms. Found 39 (131 requested) and removed 12 (65 requested) atoms. Cycle 24: After refmac, R = 0.2702 (Rfree = 0.000) for 4536 atoms. Found 29 (131 requested) and removed 15 (65 requested) atoms. Cycle 25: After refmac, R = 0.2665 (Rfree = 0.000) for 4549 atoms. Found 24 (132 requested) and removed 13 (66 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.28 2.34 NCS extension: 11 residues added (0 deleted due to clashes), 4585 seeds are put forward Round 1: 263 peptides, 41 chains. Longest chain 22 peptides. Score 0.455 Round 2: 262 peptides, 39 chains. Longest chain 13 peptides. Score 0.474 Round 3: 263 peptides, 38 chains. Longest chain 18 peptides. Score 0.487 Round 4: 261 peptides, 35 chains. Longest chain 18 peptides. Score 0.514 Round 5: 244 peptides, 36 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 4 Chains 35, Residues 226, Estimated correctness of the model 77.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9248 restraints for refining 4448 atoms. 8379 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2895 (Rfree = 0.000) for 4448 atoms. Found 100 (129 requested) and removed 30 (64 requested) atoms. Cycle 27: After refmac, R = 0.2769 (Rfree = 0.000) for 4516 atoms. Found 53 (131 requested) and removed 20 (65 requested) atoms. Cycle 28: After refmac, R = 0.2681 (Rfree = 0.000) for 4548 atoms. Found 31 (131 requested) and removed 8 (65 requested) atoms. Cycle 29: After refmac, R = 0.2644 (Rfree = 0.000) for 4568 atoms. Found 28 (132 requested) and removed 14 (66 requested) atoms. Cycle 30: After refmac, R = 0.2623 (Rfree = 0.000) for 4581 atoms. Found 36 (132 requested) and removed 32 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.28 2.34 NCS extension: 17 residues added (1 deleted due to clashes), 4615 seeds are put forward Round 1: 230 peptides, 38 chains. Longest chain 13 peptides. Score 0.404 Round 2: 246 peptides, 35 chains. Longest chain 17 peptides. Score 0.479 Round 3: 252 peptides, 32 chains. Longest chain 15 peptides. Score 0.525 Round 4: 257 peptides, 34 chains. Longest chain 21 peptides. Score 0.516 Round 5: 252 peptides, 34 chains. Longest chain 16 peptides. Score 0.504 Taking the results from Round 3 Chains 32, Residues 220, Estimated correctness of the model 78.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9318 restraints for refining 4448 atoms. 8470 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2892 (Rfree = 0.000) for 4448 atoms. Found 113 (129 requested) and removed 31 (64 requested) atoms. Cycle 32: After refmac, R = 0.2789 (Rfree = 0.000) for 4529 atoms. Found 56 (131 requested) and removed 16 (65 requested) atoms. Cycle 33: After refmac, R = 0.2725 (Rfree = 0.000) for 4568 atoms. Found 35 (132 requested) and removed 12 (66 requested) atoms. Cycle 34: After refmac, R = 0.2697 (Rfree = 0.000) for 4589 atoms. Found 19 (133 requested) and removed 13 (66 requested) atoms. Cycle 35: After refmac, R = 0.2650 (Rfree = 0.000) for 4593 atoms. Found 33 (133 requested) and removed 10 (66 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.29 2.35 NCS extension: 0 residues added, 4624 seeds are put forward Round 1: 253 peptides, 45 chains. Longest chain 15 peptides. Score 0.384 Round 2: 265 peptides, 39 chains. Longest chain 19 peptides. Score 0.482 Round 3: 266 peptides, 38 chains. Longest chain 18 peptides. Score 0.495 Round 4: 259 peptides, 39 chains. Longest chain 20 peptides. Score 0.467 Round 5: 252 peptides, 37 chains. Longest chain 14 peptides. Score 0.472 Taking the results from Round 3 Chains 38, Residues 228, Estimated correctness of the model 75.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9205 restraints for refining 4446 atoms. 8294 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2866 (Rfree = 0.000) for 4446 atoms. Found 118 (129 requested) and removed 34 (64 requested) atoms. Cycle 37: After refmac, R = 0.2765 (Rfree = 0.000) for 4530 atoms. Found 54 (131 requested) and removed 17 (65 requested) atoms. Cycle 38: After refmac, R = 0.2687 (Rfree = 0.000) for 4565 atoms. Found 35 (132 requested) and removed 10 (66 requested) atoms. Cycle 39: After refmac, R = 0.2651 (Rfree = 0.000) for 4590 atoms. Found 18 (133 requested) and removed 7 (66 requested) atoms. Cycle 40: After refmac, R = 0.2622 (Rfree = 0.000) for 4599 atoms. Found 22 (133 requested) and removed 6 (66 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.28 2.34 NCS extension: 8 residues added (1 deleted due to clashes), 4635 seeds are put forward Round 1: 207 peptides, 32 chains. Longest chain 20 peptides. Score 0.413 Round 2: 222 peptides, 33 chains. Longest chain 16 peptides. Score 0.441 Round 3: 221 peptides, 33 chains. Longest chain 23 peptides. Score 0.438 Round 4: 219 peptides, 30 chains. Longest chain 23 peptides. Score 0.468 Round 5: 221 peptides, 30 chains. Longest chain 23 peptides. Score 0.473 Taking the results from Round 5 Chains 30, Residues 191, Estimated correctness of the model 73.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 34827 reflections ( 98.30 % complete ) and 9472 restraints for refining 4448 atoms. 8738 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2805 (Rfree = 0.000) for 4448 atoms. Found 117 (129 requested) and removed 18 (64 requested) atoms. Cycle 42: After refmac, R = 0.2682 (Rfree = 0.000) for 4546 atoms. Found 56 (131 requested) and removed 14 (65 requested) atoms. Cycle 43: After refmac, R = 0.2596 (Rfree = 0.000) for 4588 atoms. Found 30 (133 requested) and removed 7 (66 requested) atoms. Cycle 44: After refmac, R = 0.2545 (Rfree = 0.000) for 4609 atoms. Found 25 (133 requested) and removed 8 (66 requested) atoms. Cycle 45: After refmac, R = 0.2516 (Rfree = 0.000) for 4626 atoms. Found 20 (134 requested) and removed 11 (67 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.29 2.35 NCS extension: 21 residues added (1 deleted due to clashes), 4665 seeds are put forward Round 1: 220 peptides, 39 chains. Longest chain 12 peptides. Score 0.364 Round 2: 225 peptides, 33 chains. Longest chain 23 peptides. Score 0.448 Round 3: 245 peptides, 38 chains. Longest chain 23 peptides. Score 0.443 Round 4: 246 peptides, 37 chains. Longest chain 17 peptides. Score 0.457 Round 5: 250 peptides, 36 chains. Longest chain 23 peptides. Score 0.478 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 214, Estimated correctness of the model 74.0 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2gfg-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 34827 reflections ( 98.30 % complete ) and 8939 restraints for refining 4454 atoms. 8063 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2797 (Rfree = 0.000) for 4454 atoms. Found 0 (129 requested) and removed 7 (64 requested) atoms. Cycle 47: After refmac, R = 0.2721 (Rfree = 0.000) for 4447 atoms. Found 0 (129 requested) and removed 2 (64 requested) atoms. Cycle 48: After refmac, R = 0.2696 (Rfree = 0.000) for 4444 atoms. Found 0 (128 requested) and removed 5 (64 requested) atoms. Cycle 49: After refmac, R = 0.2677 (Rfree = 0.000) for 4438 atoms. TimeTaking 54.83