Sun 23 Dec 22:23:10 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 2o2g-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-1.9-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/2o2g-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-1.9-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 22:23:20 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/2o2g-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-1.9-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 197 and 0 Target number of residues in the AU: 197 Target solvent content: 0.4756 Checking the provided sequence file Detected sequence length: 223 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 223 Adjusted target solvent content: 0.41 Input MTZ file: 2o2g-1.9-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: 19 Cell parameters: 47.887 62.444 67.988 90.000 90.000 90.000 Input sequence file: 2o2g-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 1784 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 Loops will be built when appropriate and at the last cycle Resolution range: 45.990 1.920 Wilson plot Bfac: 18.79 15016 reflections ( 93.16 % complete ) and 0 restraints for refining 1993 atoms. Observations/parameters ratio is 1.88 ------------------------------------------------------ Starting model: R = 0.3951 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3515 (Rfree = 0.000) for 1993 atoms. Found 45 (76 requested) and removed 52 (38 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.12 2.39 Round 1: 87 peptides, 19 chains. Longest chain 7 peptides. Score 0.265 Round 2: 94 peptides, 17 chains. Longest chain 10 peptides. Score 0.392 Round 3: 101 peptides, 17 chains. Longest chain 11 peptides. Score 0.445 Round 4: 102 peptides, 15 chains. Longest chain 11 peptides. Score 0.513 Round 5: 110 peptides, 17 chains. Longest chain 13 peptides. Score 0.509 Taking the results from Round 4 Chains 15, Residues 87, Estimated correctness of the model 83.4 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 3608 restraints for refining 1742 atoms. 3248 conditional restraints added. Observations/parameters ratio is 2.15 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3696 (Rfree = 0.000) for 1742 atoms. Found 50 (67 requested) and removed 34 (33 requested) atoms. Cycle 2: After refmac, R = 0.3593 (Rfree = 0.000) for 1751 atoms. Found 39 (67 requested) and removed 34 (33 requested) atoms. Cycle 3: After refmac, R = 0.3454 (Rfree = 0.000) for 1751 atoms. Found 28 (67 requested) and removed 30 (33 requested) atoms. Cycle 4: After refmac, R = 0.3368 (Rfree = 0.000) for 1747 atoms. Found 30 (67 requested) and removed 20 (33 requested) atoms. Cycle 5: After refmac, R = 0.3207 (Rfree = 0.000) for 1755 atoms. Found 31 (67 requested) and removed 15 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.94 2.19 Round 1: 91 peptides, 14 chains. Longest chain 14 peptides. Score 0.467 Round 2: 99 peptides, 12 chains. Longest chain 17 peptides. Score 0.581 Round 3: 104 peptides, 13 chains. Longest chain 24 peptides. Score 0.584 Round 4: 103 peptides, 14 chains. Longest chain 22 peptides. Score 0.549 Round 5: 103 peptides, 12 chains. Longest chain 26 peptides. Score 0.605 Taking the results from Round 5 Chains 12, Residues 91, Estimated correctness of the model 88.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 3703 restraints for refining 1742 atoms. 3351 conditional restraints added. Observations/parameters ratio is 2.15 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3396 (Rfree = 0.000) for 1742 atoms. Found 60 (67 requested) and removed 23 (33 requested) atoms. Cycle 7: After refmac, R = 0.3192 (Rfree = 0.000) for 1778 atoms. Found 34 (68 requested) and removed 10 (34 requested) atoms. Cycle 8: After refmac, R = 0.3027 (Rfree = 0.000) for 1801 atoms. Found 46 (69 requested) and removed 8 (34 requested) atoms. Cycle 9: After refmac, R = 0.2911 (Rfree = 0.000) for 1834 atoms. Found 24 (70 requested) and removed 17 (35 requested) atoms. Cycle 10: After refmac, R = 0.2890 (Rfree = 0.000) for 1837 atoms. Found 28 (70 requested) and removed 3 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.92 2.17 Round 1: 105 peptides, 18 chains. Longest chain 13 peptides. Score 0.443 Round 2: 112 peptides, 15 chains. Longest chain 16 peptides. Score 0.578 Round 3: 116 peptides, 15 chains. Longest chain 22 peptides. Score 0.602 Round 4: 116 peptides, 16 chains. Longest chain 14 peptides. Score 0.575 Round 5: 119 peptides, 15 chains. Longest chain 24 peptides. Score 0.619 Taking the results from Round 5 Chains 15, Residues 104, Estimated correctness of the model 89.4 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 3572 restraints for refining 1774 atoms. 3152 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3265 (Rfree = 0.000) for 1774 atoms. Found 57 (68 requested) and removed 22 (34 requested) atoms. Cycle 12: After refmac, R = 0.3113 (Rfree = 0.000) for 1809 atoms. Found 45 (69 requested) and removed 10 (34 requested) atoms. Cycle 13: After refmac, R = 0.2947 (Rfree = 0.000) for 1842 atoms. Found 34 (70 requested) and removed 10 (35 requested) atoms. Cycle 14: After refmac, R = 0.2871 (Rfree = 0.000) for 1865 atoms. Found 37 (71 requested) and removed 4 (35 requested) atoms. Cycle 15: After refmac, R = 0.2840 (Rfree = 0.000) for 1898 atoms. Found 34 (73 requested) and removed 11 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.91 2.16 Round 1: 102 peptides, 15 chains. Longest chain 14 peptides. Score 0.513 Round 2: 112 peptides, 16 chains. Longest chain 18 peptides. Score 0.550 Round 3: 113 peptides, 15 chains. Longest chain 14 peptides. Score 0.584 Round 4: 114 peptides, 15 chains. Longest chain 18 peptides. Score 0.590 Round 5: 106 peptides, 13 chains. Longest chain 14 peptides. Score 0.596 Taking the results from Round 5 Chains 13, Residues 93, Estimated correctness of the model 88.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 3721 restraints for refining 1814 atoms. 3362 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3094 (Rfree = 0.000) for 1814 atoms. Found 69 (69 requested) and removed 14 (34 requested) atoms. Cycle 17: After refmac, R = 0.2933 (Rfree = 0.000) for 1869 atoms. Found 53 (71 requested) and removed 11 (35 requested) atoms. Cycle 18: After refmac, R = 0.2864 (Rfree = 0.000) for 1910 atoms. Found 35 (73 requested) and removed 6 (36 requested) atoms. Cycle 19: After refmac, R = 0.2767 (Rfree = 0.000) for 1937 atoms. Found 24 (74 requested) and removed 7 (37 requested) atoms. Cycle 20: After refmac, R = 0.2714 (Rfree = 0.000) for 1954 atoms. Found 35 (75 requested) and removed 4 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.90 2.14 Round 1: 107 peptides, 13 chains. Longest chain 19 peptides. Score 0.602 Round 2: 109 peptides, 13 chains. Longest chain 22 peptides. Score 0.613 Round 3: 98 peptides, 14 chains. Longest chain 12 peptides. Score 0.516 Round 4: 109 peptides, 12 chains. Longest chain 22 peptides. Score 0.639 Round 5: 95 peptides, 14 chains. Longest chain 12 peptides. Score 0.496 Taking the results from Round 4 Chains 12, Residues 97, Estimated correctness of the model 90.4 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 3751 restraints for refining 1890 atoms. 3333 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2939 (Rfree = 0.000) for 1890 atoms. Found 72 (72 requested) and removed 22 (36 requested) atoms. Cycle 22: After refmac, R = 0.2858 (Rfree = 0.000) for 1940 atoms. Found 48 (74 requested) and removed 8 (37 requested) atoms. Cycle 23: After refmac, R = 0.2683 (Rfree = 0.000) for 1980 atoms. Found 43 (76 requested) and removed 9 (38 requested) atoms. Cycle 24: After refmac, R = 0.2602 (Rfree = 0.000) for 2013 atoms. Found 39 (77 requested) and removed 7 (38 requested) atoms. Cycle 25: After refmac, R = 0.2563 (Rfree = 0.000) for 2043 atoms. Found 44 (78 requested) and removed 9 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.91 2.16 Round 1: 106 peptides, 13 chains. Longest chain 18 peptides. Score 0.596 Round 2: 98 peptides, 12 chains. Longest chain 18 peptides. Score 0.575 Round 3: 92 peptides, 11 chains. Longest chain 13 peptides. Score 0.566 Round 4: 94 peptides, 13 chains. Longest chain 13 peptides. Score 0.519 Round 5: 102 peptides, 13 chains. Longest chain 13 peptides. Score 0.572 Taking the results from Round 1 Chains 15, Residues 93, Estimated correctness of the model 88.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 4007 restraints for refining 1962 atoms. 3606 conditional restraints added. Observations/parameters ratio is 1.91 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2832 (Rfree = 0.000) for 1962 atoms. Found 74 (75 requested) and removed 16 (37 requested) atoms. Cycle 27: After refmac, R = 0.2731 (Rfree = 0.000) for 2020 atoms. Found 56 (77 requested) and removed 8 (38 requested) atoms. Cycle 28: After refmac, R = 0.2656 (Rfree = 0.000) for 2067 atoms. Found 45 (79 requested) and removed 10 (39 requested) atoms. Cycle 29: After refmac, R = 0.2597 (Rfree = 0.000) for 2100 atoms. Found 40 (80 requested) and removed 14 (40 requested) atoms. Cycle 30: After refmac, R = 0.2560 (Rfree = 0.000) for 2125 atoms. Found 41 (81 requested) and removed 16 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.90 2.14 Round 1: 96 peptides, 14 chains. Longest chain 13 peptides. Score 0.503 Round 2: 102 peptides, 15 chains. Longest chain 12 peptides. Score 0.513 Round 3: 102 peptides, 15 chains. Longest chain 13 peptides. Score 0.513 Round 4: 100 peptides, 13 chains. Longest chain 12 peptides. Score 0.559 Round 5: 104 peptides, 14 chains. Longest chain 12 peptides. Score 0.556 Taking the results from Round 4 Chains 13, Residues 87, Estimated correctness of the model 86.1 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 4144 restraints for refining 2005 atoms. 3787 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2820 (Rfree = 0.000) for 2005 atoms. Found 75 (77 requested) and removed 16 (38 requested) atoms. Cycle 32: After refmac, R = 0.2675 (Rfree = 0.000) for 2063 atoms. Found 55 (79 requested) and removed 15 (39 requested) atoms. Cycle 33: After refmac, R = 0.2564 (Rfree = 0.000) for 2102 atoms. Found 43 (80 requested) and removed 8 (40 requested) atoms. Cycle 34: After refmac, R = 0.2505 (Rfree = 0.000) for 2136 atoms. Found 40 (82 requested) and removed 8 (41 requested) atoms. Cycle 35: After refmac, R = 0.2463 (Rfree = 0.000) for 2168 atoms. Found 42 (83 requested) and removed 9 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.88 2.12 Round 1: 109 peptides, 16 chains. Longest chain 12 peptides. Score 0.531 Round 2: 110 peptides, 12 chains. Longest chain 24 peptides. Score 0.644 Round 3: 108 peptides, 14 chains. Longest chain 13 peptides. Score 0.581 Round 4: 112 peptides, 15 chains. Longest chain 12 peptides. Score 0.578 Round 5: 113 peptides, 13 chains. Longest chain 13 peptides. Score 0.636 Taking the results from Round 2 Chains 12, Residues 98, Estimated correctness of the model 90.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 4153 restraints for refining 2054 atoms. 3773 conditional restraints added. Observations/parameters ratio is 1.83 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2777 (Rfree = 0.000) for 2054 atoms. Found 79 (79 requested) and removed 14 (39 requested) atoms. Cycle 37: After refmac, R = 0.2626 (Rfree = 0.000) for 2119 atoms. Found 57 (81 requested) and removed 6 (40 requested) atoms. Cycle 38: After refmac, R = 0.2536 (Rfree = 0.000) for 2170 atoms. Found 55 (83 requested) and removed 12 (41 requested) atoms. Cycle 39: After refmac, R = 0.2476 (Rfree = 0.000) for 2209 atoms. Found 40 (85 requested) and removed 14 (42 requested) atoms. Cycle 40: After refmac, R = 0.2430 (Rfree = 0.000) for 2233 atoms. Found 39 (86 requested) and removed 13 (43 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.89 2.13 Round 1: 107 peptides, 14 chains. Longest chain 12 peptides. Score 0.575 Round 2: 111 peptides, 12 chains. Longest chain 25 peptides. Score 0.650 Round 3: 112 peptides, 14 chains. Longest chain 13 peptides. Score 0.605 Round 4: 123 peptides, 14 chains. Longest chain 19 peptides. Score 0.664 Round 5: 110 peptides, 14 chains. Longest chain 12 peptides. Score 0.593 Taking the results from Round 4 Chains 14, Residues 109, Estimated correctness of the model 91.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15016 reflections ( 93.16 % complete ) and 4228 restraints for refining 2100 atoms. 3806 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2746 (Rfree = 0.000) for 2100 atoms. Found 80 (80 requested) and removed 27 (40 requested) atoms. Cycle 42: After refmac, R = 0.2646 (Rfree = 0.000) for 2153 atoms. Found 67 (82 requested) and removed 9 (41 requested) atoms. Cycle 43: After refmac, R = 0.2512 (Rfree = 0.000) for 2211 atoms. Found 54 (85 requested) and removed 8 (42 requested) atoms. Cycle 44: After refmac, R = 0.2445 (Rfree = 0.000) for 2255 atoms. Found 36 (86 requested) and removed 9 (43 requested) atoms. Cycle 45: After refmac, R = 0.2395 (Rfree = 0.000) for 2280 atoms. Found 48 (87 requested) and removed 13 (43 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.87 2.11 Round 1: 100 peptides, 12 chains. Longest chain 21 peptides. Score 0.587 Round 2: 100 peptides, 12 chains. Longest chain 16 peptides. Score 0.587 Round 3: 100 peptides, 11 chains. Longest chain 25 peptides. Score 0.615 Round 4: 106 peptides, 11 chains. Longest chain 27 peptides. Score 0.648 Round 5: 104 peptides, 11 chains. Longest chain 25 peptides. Score 0.637 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 95, Estimated correctness of the model 90.8 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2o2g-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15016 reflections ( 93.16 % complete ) and 4321 restraints for refining 2160 atoms. 3925 conditional restraints added. Observations/parameters ratio is 1.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2580 (Rfree = 0.000) for 2160 atoms. Found 0 (83 requested) and removed 5 (41 requested) atoms. Cycle 47: After refmac, R = 0.2503 (Rfree = 0.000) for 2154 atoms. Found 0 (82 requested) and removed 2 (41 requested) atoms. Cycle 48: After refmac, R = 0.2502 (Rfree = 0.000) for 2152 atoms. Found 0 (82 requested) and removed 1 (41 requested) atoms. Cycle 49: After refmac, R = 0.2493 (Rfree = 0.000) for 2151 atoms. TimeTaking 32.45